It’s true that the Romer Court said the amendment (to Colorado’s constitution) did not even withstand rational basis review. However, it was still an equal protection case, and the Court’s main concern was that the amendment was class-based legislation that disadvantaged an unpopular group.
Given the Court’s strong language in this regard, I think there’s no question that if they’d skipped the rational basis test or actually found it to have a rational basis then they would have applied strict scrutiny and overturned the amendment on that basis. So Winsdor did go beyond Romer by applying a heightened form of scrutiny, but not by much.