My thinking behind Charles V creating a kingdom for Ferdinand in TTL was to transform the many lands of the Burgundian inheritance into a unified entity. In OTL, Charles issued the Pragmatic Sanction of 1549 in order to streamline the succession laws of all Seventeen Provinces and I could see him wanting to give Ferdinand a kingdom to match the titles Philip II would inherit in TTL.
In TTL, Ferdinand would have probably been made regent of the Netherlands by Charles in this TTL before inheriting them. In OTL, Charles took Philip to Germany to introduce Philip to various princes in the Empire and made his daughter Maria and nephew/son in law regents of Spain in his absence. In TTL, Charles could have also used that time to introduce Ferdinand to his future domain and have his sister Mary train him in his future responsibilities. Regardless of what title Charles is able to grant Ferdinand in TTL, there will most likely be a rivalry between the Burgundian Habsburgs and their cousins in Vienna for the imperial throne. The Burgundian inheritance would make Ferdinand the wealthiest prince in the Empire, a prince rich enough to influence imperial elections.
The wife of Ferdinand in TTL could be any number of interesting candidates. If his brother Philip still marries Mary I of England in TTL, then perhaps Charles V would be able to convince Mary to betroth Elizabeth, her sister and heir, to Ferdinand. In OTL, Mary did not want Elizabeth to marry anyone because it would have required Elizabeth to made legitimate by the Pope, which would have called Mary’s own legitimacy into question, so I cannot see Mary ever allowing Elizabeth to marry anyone. Perhaps Elizabeth falls in love with Ferdinand “the Fair” at her sister’s wedding and marries him when she becomes queen. I guess I am looking for any excuse to form a personal union of England and Burgundy.
The relationship between Philip and Ferdinand in TTL would be fascinating. Even though they would both be raised in a similar manner, Ferdinand would probably be more tolerant than Philip was in OTL in his handling of the Netherlands. Imagine a Spain that does not bankrupt itself multiple times trying to pacify the Netherlands. Burgundy would still need the protection of Spain to defend itself against France in TTL.