First, the Government Accountability Office report should not be used to show an "association" with rights and benefits of marriage. That report only shows that marriage status is a factor in 1049 places in the United States Code (USC) or the updated GAO report that finds 1138 instances in the USC. The report was commissioned in response to the Defense of Marriage Act, which defined marriage as a legal union between one man and one woman.
In connection with the enactment of the Defense of Marriage Act, you asked us, in your September 5, 1996, letter, to identify federal laws in which benefits, rights, and privileges are contingent on marital status. Your staff agreed that we should identify more generally all those laws in the United States Code in which marital status is a factor, even though some of these laws may not directly create benefits, rights, or privileges.
The report also warns against using it to draw conclusions that it prohibits people in same-sex marriages, people in same-sex civil unions, or single people from enjoying benefits and rights available to people in opposite-sex marriages under federal law.
Finally, no conclusions can be drawn, from our identification of a law as one in which marital status is a factor, concerning the effect of the law on married people versus single people. A particular law may create either advantages or disadvantages for those who are married, or may apply to both married and single people.
As far as your questions go:
if it's economic, than why aren't those benefits extended to any set of roommates?
Because, that is the way the law was written. In general, we have many laws that understand the strong bonds between family members and recognize and promote families. Some laws would make little sense to extend to room-mates, for example the estate laws. Married persons usually share property jointly, mingle their funds, and share obligations. Married persons are allowed an unlimited exemption when transfering property upon death to their surviving spouse. This exemption doesn't affect many people, (you already can transfer $5 million to any individual), and isn't applicable to non-citizens. If the government extended the benefit to roommates, you could imagine the number of one month leases that would occur to take advantage of the tax loophole.
if it's custody-related why aren't those benefits extended to unmarried parents?
First off, unmarried parents do have benefits extends to them, even in cases that many people would object to. Legal guardians, parents being an example of one, are granted benefits and responsibilities to their children (and in many cases, even children which aren't theirs). Unmarried parents don't have a legally recognized relationship, and therefore don't have any of the legal benefits or responsibilities related to the children in a marriage.