As I say, I'm not familiar with Spanish law, so I honestly don't know, but if not you have the same problem that exists here: A civil and religious institution that share the same name, as well as many of the same attributes, despite being wholly separate practices.

Not that it really matters anyway because as far as the Pope is concerned such distinctions are meaningless; in the eyes of the Catholic Church you were either married within the Catholic Church (e.g. sacramentally) or you aren't married. There's no reason why the Pope should find homosexuals in the latter state any more objectionable than anyone else in it, but from the perspective the Pope is REQUIRED to take, "gay marriage" has no more standing than "Islamic marriage".