Both sentences in your question are correct and they mean the same thing. The syntax is different.
Because X may take different forms, a priori so would Y.
There's nothing ungrammatical about a priori here. It's functioning as an adverb meaning "based on theoretical deduction". As for so would Y, it is a construct used to express agreement with what has been mentioned before in the sentence. In a dialogue where you can have exactly the same construct it would sound more natural:
A: "I would definitely choose the red shirt over the yellow one."
B: "So would I."
When so is placed in the beginning of a sentence or a clause to express agreement, there is inversion between the auxiliary verb and the subject, in other words you write the subject-auxiliary verb in question form. The main verb is omitted. This is a shorter way of saying I would do the same thing.