You make good points, of course, but I'm still unconvinced. Philip's marriages, unlike Henry VIII, were all political, to gain a strategic or psychological advantage (by tying himself to a rival dynasty), whereas with Liz defeated he had little to gain. Liz was well past childbearing age, so a marriage to her would serve little traditional purpose, and by this point she had already tied herself down with her speeches about being married to her kingdom, which she declared herself to be uniquely devoted to. Also, the Protestant cause is effectively ended, at least inasmuch as it will be relegated to the status of hunted religion as Catholicism was in OTL England, given London falling. Marrying Philip wouldn't help secure their status, Phil would use it to force her conversion, depriving England of both a leader and a potential martyr - which Liz was quite happy to be if it advanced the Protestant cause. And Philip had given his (claimed) crown of England to his (Catholic) daughter so he wouldn't be exerting any control there anyway. Likely she would be carted back to him in Spain, where he could make sure that she could no longer cause him any trouble.
Again, I see your point, I'm just not quite sure I see it the same way. I guess it's possible, though.