The DOMA case is different as that was the federal government interfering with the affairs of the states. It was intended to undermine the laws of the states on a matter where the federal government had no constitutional authority.
#1 Excuse me, you said "No one is being penalized by non-recognition of gay marriage.", the Windsor case expressly disproves that claim in that Windsor would have been subject to over $350,000 in taxes specifically because their marriage wasn't recognized. States also have income taxes, pension benefits, empployer health insurance, the concept of "assumed parentage" on the birth of a child***, seemless (untaxed) transfer of property between spouses, "family" rates for spouses [in terms of home, auto, life, health, etc. insurance], recognition of the family relationship of a spouse in various legal matters including wrongful death, State tuition calculations for instate post-high school schools, equitable distribution of property in case of a divorce, default medical decision power as the default next-of-kin in the case of an accident and lacking a Medical Power of Attorney, etc., etc.
#2 DOMA did nothing to interfere with State tax law, it was based on Federal tax law.
#3 How could DOMA be passed to undermine the laws of the States, in 1996 when it was passed there were no States with Same-sex Civil Marriage.
#4 Article 1 Section 4 (Full Faith and Credit Clause) expressly grants Congress the power to determine the effect of public acts between the States (of which Civil Marriage is a public act) and the 16th Amendment allows the Federal government to lay and collect taxes on income. Section 2 of DOMA (which still stands BTW) falls under Article I Section 4 and Federal Tax law falls under the 16th Amendment (which impacted Section 3, the part found unconstitutional).
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*** This means that the spouses in a Civil Marriage are the legal parents upon of the birth of a child something recognized in all 50 States for different sex couples. A marriage different sex couple in California has a child, they are both legally the parents at the time of birth. They travel to Virginia, they are still both the legal parents. However for a legally marriage same-sex couple, the law doesn't function the same. Virginia passed a State Constitutional amendment barring not only Civil Marriage but any legal actions that attempt to recreate the benefits of Civil Marriage. A different-sex couple are married, they have a child, they are both the legal parents. If that couple were to visit Virginia, the non-biological parent would no longer have legal parent status as the basis of that parentage is a legal marriage that Virginia considers invalid.
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