While it is true most people in Puerto Rico were not actively interested in pursuing independence, they did rebel in 1868 and proclaimed a short-lived republic in response to the repressive and ineffective government of Isabel II.
There was certainly a push towards more autonomy, not necessarily integration, at least back then. They even got a constitution from Spain. They wanted to be left to govern themselves under the protection of another power.
Spanish Puerto Rico was very neglected, its value being more sentimental than economic, unlike Cuba, which if I recall correctly, was the wealthiest Spanish territory, Puerto Rico was a backwater, with only one good port, and a mostly mountainous terrain. Emigration will continue no matter who owns it. The economy is not big enough to sustain a high population.
Assuming Spain keeps Cuba, then all focus will be placed there. I don’t see the US allowing an alt fascist Spain keep control of Puerto Rico, even an alt Spanish Soviet-aligned republican government might be too uncomfortable. The US will apply the Panama treatment and sponsor separatism under whatever pretext they can come up with.
If for whatever reason political union survives any alt decolonization period, then sure, it could be part of Spain like French Guyana and New Caledonia are part of France.