Interestingly, if you'd want an Anglo-Spanish alliance lasting longer, it would be far more plausible for England to stay Catholic, rather than having Spain become Protestant, considering how much back-and-forth happened in England. Also, since the Habsburgs had such a close relationship with the Papacy, it would be highly unlikely that a Church of Spain would develop and split off from Rome. I guess if you were truly hell bent on having a Protestant Spain, you could have the de Trastamara dynasty remain in power and not get involved with the Habsburgs, (maybe if Johanna the Mad were born a boy?) and if Aragonese interests in Italy started souring relations with the Pope, then perhaps Spain would have indeed became Protestant.
Protestant France, on the other hand, is a much easier task. Heck, if the Wars of Religion went another way, a Protestant France could possibly have been in the cards (possibly. Not probably.

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Granted, there are major geopolitical concerns as to why an Anglo-Spanish alliance would've encountered at some point. Of course both parties were heavily invested in the idea of containing France, but both were also major colonial powers in the Atlantic world. So the alliance isn't impossible, but you'd need to figure out a way for the two to work that out.