Why do news articles often refer to the leader as opposed to the country?
Often it's because they're writing about the leader's actions, decisions, or policies rather than those attributable to the government as a whole. Another reason, in two of these three examples, is that the leaders in question have so much power that they are arguably dictators, not subject to any significant control by the legislature.
Heads of state, heads of government, and even corporate CEOs wield the power of the entity they control. Often much of the power they wield is delegated to them by the legislature or board of directors, leaving them with a good deal of personal discretion. A headline that names a leader may do so in recognition of that discretion.
Alternatively, in cases where leaders do not possess delegated authority, they may propose action to the legislature. In such cases, while the action would ultimately be taken with the legislature's approval, and therefore clearly be attributable collectively to the country's government, it is nonetheless readily identifiable as an initiative of the leader.
In the first example, people often do attribute military action to the country rather than to its military or political leaders. Headlines reporting the invasion of Poland spoke of "Germany," "German Army," "Nazi army," and "Hitler." In this case, Duterte is (I assume) both the commander in chief of the Philippine military and the source of Philippine foreign policy, so responsibility for actions of this sort really do reside with him, not with the legislature.
The second example is similar. Economic sanctions are a tool of foreign policy, and domestic economic policy is often the realm of the executive. Even if some elements of domestic economic policy (tariffs, perhaps) have to be enacted by the legislature, the impetus for changing the law will often come from the executive. The leader is the one responsible for the decisions being reported.
The third example is somewhat different. The article is cast as an analysis of Boris Johnson's premiership, which has involved other existential controversies not only threatening his party's majority in parliament but also implicating fundamental change in the UK's constitution. The principal such controversy, of course, was the departure from the European Union, which was Johnson's main issue and which has very directly led to the reinvigoration of the Scottish independence movement. The article isn't fundamentally about the UK's conflict with those who seek Scottish independence; it's about Johnson's political fortunes and about whether he can keep his commitment to UK together, whether he can manage the very serious consequences of his success in bringing about the central promise on which he was elected. In short, the headline names him because the article is about him.
unless the leader is speaking personally, they represent their country, their decisions are their country's decisions
That's true, but in writing these headlines, the papers presume that readers know that Duterte represents the Philippines, that Putin represents Russia, and that Johnson represents the United Kingdom.
To say for example that Duterte would send navy ships into the South China Sea shines the limelight on him. If it turns out well he gets all the accolades even though the members of his cabinet could deserve as much (or even more) credit; the same goes if it goes badly.
That's also true, and it's a big part of the answer to your question. These journalists have named these people in the headlines precisely because they want to put them in the limelight. In order to understand the international political stance of the Philippines or Russia, you need to understand the personality of Duterte or Putin. To understand the internal politics of the UK parliament, you need to understand Boris Johnson.