I think the big different re: Miguel da Paz is that Portugal is contingent with Castile, so it's no biggie for him to be sent to Castile, especially since he'll be the future king there and unite the peninsula. Sending Eleanor to Castile wouldn't happen immediately, since there's no way they're putting an infant onto a boat on a potentially dangerous sea voyage. 16th century ships aren't exactly known for being the most hygienic places, and even Margaret of Austria had fears of her ship sinking on her travail to Spain. I think it's likely she won't go to Spain until she's old enough and strong enough for the voyage, which will give Philip enough time to remarry and have a son and secure the Burgundian succession. I could see her going in 1503-1504, which is pushing it IMO and probably the absolute earliest she could go.
In the mean time, I could see Isabella ensuring she has say over Eleanor's education during those few years she's still in the Low Countries and would probably try and build up a Spanish suite around her. At the very least, she'll be coming to Spain young enough that she'll be reared and raised as a Castilian, much how Ferdinand turned out IOTL.
Agreed. So the education would remain the flash point. Ferdinand and Isabella would probably want to send Spanish courtiers to Brussels to ensure Eleanor can speak spanish and be familiar with her future realm. But Philip is in the position to block their access to the child if he starts making demands or just wants to be petty.
As regards Alfonso of Ampurias as a candidate for Eleanor if they wanted a Trastamara for her wouldn't Frederick of Naples' son Ferdinand be a better choice? I know his father had been deposed but he's still a Trastamara and he would secure the claim to Naples in a period when its still be contested with France.