Ok I’ll admit I’m not the most knowledgeable on Habsburg history in the 16th century, but I know enough to know that if Charles had a second son that there would be some implications). I heard that Charles intend to have his second son receive the Burgundian inheritance. Other than that, what would the effects be, who would he marry, what would France do about another Habsburg on the Burgundian throne, etc?
So you are talking about the 3 way split: Spain, colonies and Italian possessions to Phillip, Bohemia, Austria, leftover of Hungary and imperial crown to Charles' brother, and the Netherlands with French Comte to the 2nd son? Who inherits Charles' debt? In OTL it was Phillip would in your AH could it be split between the brothers?
(a) Spain eventually gains from not dealing with the rebellious Provinces but it leaves an open field for screwing up economically by keeping interfering in the European affairs.
(b) Imperial branch - more or less as in OTL. Differences may start closer to the time of the 30YW.
(c) The "Burgundian" branch, if left alone, may be in a worse position against France if there is an earlier peace between France and Spain. Would have to look for the alliances close to home: either imperial Hapsburgs or, in an
unlikely political step, with the German Protestants. Position of a Catholic Hapsburg ruler would be in danger with a strengthening Protestantism so the ruler would have to exercise a lot of flexibility balancing between the local Protestants and Catholics. Probably some kind of an early constitutional monarchy? France would still pick up Artois and French Comte (almost impossible to defend in that schema)