Your question is not terribly clear. Moving the clause to a declaration was part of the ’de-constitutionalization’ process that led to the Lisbon Treaty, so it would appear more palatable to voters than the rejected EU Constitution. There are minor technical differences induced by this change.
However, the main confusion in your question seems to be that
the EU doesn't have a supremacy but a primacy principle. The latter means that its actual implementation depends on the good will of member countries, the EU (e.g. ECJ) cannot strike down member countries' legislation.
Primacy is not necessarily to be seen as a ‘hierarchical’ supremacy (‘higher
law’) in the sense that the validity of national law would depend on its compliance
with EU law. For instance, while the principle of primacy does impose
an obligation on the national legislature to refrain from adopting laws that are
inconsistent with EU law and a duty to modify laws that are so inconsistent,
it does not automatically render such conflicting national measures invalid or
non-existent.16 Rather, primacy imposes an obligation on all national authorities
to ‘set aside conflicting national measures’ and leave them inapplicable; hence
the emphasis, in German parlance, on the fact that EU primacy concerns only
Anwendungsvorrang and not Geltungsvorrang. The EU principle of primacy is a
conflict rule, indicating which norm should be applied where two inconsistent
norms collide.
In this respect, the EU version of primacy differs from similar principles in
federal states such as the German Bundesrecht bricht Landesrecht laid down in
Article 31 Basic Law and the Supremacy Clause under Article 6, Clause 2 of the
US Constitution. The EU principle of primacy affects only the applicability of the
conflicting national provision, not its validity, on which the EU has no direct say.
In ‘truly federal systems’ the federal organs and especially the federal courts do
have a direct say on conflicting acts of the federated entities. The EU and its Court
do not have such jurisdiction: they can only declare them in breach of EU law, and
oblige national authorities to leave them inapplicable to the extent of their inconsistency
with EU law. Accordingly, the EU is highly dependent on the cooperation
of the national authorities to heed and actually set aside inconsistent measures
of national law.
Why primacy and not supremacy is rather simple: many member countries would not agree with outright EU supremacy. I don't think supremacy was ever proposed at EU level.
As a result each EU country has its own doctrinal peculiarities in how it interprets EU primacy. These are far too long to detail here; see the reference below for details. As a general idea: some countries have crafted narrow escape clauses in their constitutions, others use procedural mechanisms to reaffirm primacy, others rely just on their domestic case law (typically at national supreme court level). To give you a relatively simple example:
Article 29.4.6 of the Irish Constitution grants constitutional immunity to
European law and to Irish laws enacted, acts done, and measures adopted that
are necessitated by the obligations of membership. The provision intends to
limit the reach of the Constitution, and prevents the courts from reviewing the
constitutionality of EU law, and of Irish law necessitated by the obligations of
membership, thus ensuring the primacy of EU law over the Irish Constitution.
Nevertheless, in SPUC v Grogan, a case concerning the particularly sensitive issue
of abortion, Walsh J stated in the High Court that ‘it cannot be one of the objectives
of the European Communities that a Member State should be obliged to
permit activities which are clearly designed to set at nought the constitutional
guarantees for the protection within the State of a fundamental human right’. So
despite the constitutional immunity granted to EU law in the constitutional texts,
courts feel uneasy about actually awarding primacy to EU law in cases where it
appears to be at odds with fundamental values protected in the Constitution, such
as fundamental rights.
The same argument is even more persuasively and more effectively put
forward in those countries where the primacy of EU law is not built on an
explicit constitutional authorization, but on a reinterpretation of the existing
text of the Constitution, usually a transfer of powers or limitation of sovereignty
clause.
Examples of the latter include Italy and Germany (law details omitted here, see the reference for that). Clearly since core members such as Italy and Germany would only agree with a primacy with some escape clause, they would not agree to outright supremacy. Another short example is Sweden:
Art 6 of Chapter 10 of the Instrument of Government: ‘Within the framework of European
Union cooperation, the Riksdag may transfer decision-making authority which does not affect the
basic principles by which Sweden is governed. Such transfer presupposes that protection for rights
and freedoms in the field of cooperation to which the transfer relates corresponds to that afforded
under this Instrument of Government and the European Convention for the Protection of Human
Rights and Fundamental Freedoms.’
As for some examples of the last kind
in addition to the German
and the Italian constitutional courts, the Spanish Tribunal constitucional, the
Danish Højesteret, and the Polish Trybunal Konstytucyjny have announced
that in exceptional circumstances, where EU law interferes with fundamental
principles of the [national] Constitution, it will not be applicable
The [national law] cases are cited in the reference.
So I hope you can see why the exact format of the primacy clause at EU level isn't a huge issue. It ultimately depends on member countries to interpret and apply it. When the (failed) EU Constitution was proposed, there was a tempest in a teapot in France and Spain with respect to primacy:
The provision caused quite a stir among both
the conventioners and the general public. In order to convince them that such
primacy was in fact only the confirmation of the existing situation, a Declaration
was added to the Treaty, stating that Article I-6 reflected the existing case law
of the Court and did not essentially alter the existing situation. The provision
played an important role in the decisions of both the French and the Spanish
constitutional courts on the Constitutional Treaty. Both discussed the provision
as one of the elements of the Treaty that might change the nature of the Union
and make it unconstitutional for the state to adhere to such a Treaty. Both arrived
at the conclusion that it did not and that the provision did not alter the nature
of the Treaty or the status of the national Constitution as the supreme norm
of the land. Both courts also paid particular attention to the national identity
clause immediately preceding the primacy provision in Article I-5 to arrive at
that conclusion. The French Conseil constitutionnel, moreover, emphasized that
the scope of the principle remained the same and was duly accepted by Article
88-1 of the Constitution. The Spanish Tribunal constitucional insisted on the
difference between the supremacy of the Constitution and the primacy of EU
law. Effectively, both courts opined that Article I-6 did not change the nature of
the Union.
As you can see both countries concluded that the explicit inclusion in the (ultimately non-ratified) Constitution didn't really make any difference over prior arrangements. No other countries even raised concerns, apparently.