Well...Elizabeth would be more likely to produce half-Tudor Habsburg babies than Mary was OTL, BUT HVIII isn't going to let his younger "bastard" daughter marry before his older "bastard" daughter. So, I think one of Mary's betrothals needs to come off - perhaps to the ill-fated dauphin during days of a French alliance? Although, I'm not sure when that might be without keeping Anne Boleyn around longer (maybe after Jane Seymour's death? When Henry was considering a French match for wife no. 4), or to the duke of Beja if we're going imperial.
The thing is, Elizabeth was mooted for several Habsburg and Habsburg-related princes (Felipe II of Spain, Archduke Ferdinand II and Archduke Karl of Austria, the duke of Savoy, a Portuguese infante (I assume Prince Joao) and the duque de Segorbe) before and after Mary's reign. However, it's a long way from bended knee to altar steps, but Liz's perceived illegitimacy might not be the reason the plans get scuppered.
Hell, I know this was more to block against the pro-French queen of Scots, but Felipe had no problem with legitimacy when he was considering her as a wife should her sister die in childbed.
That said, it would make for interesting offspring.