Punctuation of compound predicate where the first item ends in a list?
Solution 1:
Strictly speaking, there should be no comma before and in your second example, because, as you say, and learn Y is not a full clause, but an elliptical clause: the words the projects was created to would need to be supplied to 'solve' the ellipsis:
The project was created to practice V, W, and X and [the project was created to] learn Y.
Elliptical sentences are generally not preceded by a comma, to indicate that they have a strong conexion with the first clause of the sentence.
However, this rule is not generally interpreted to be 100% strict: if a comma feels appropriate, most readers will probably accept it. One reason to add a comma could be to separate two very long clauses (which does not apply to your examples).
Another reason could be that the elliptical clause is viewed as an afterthought, which generally gets a comma. When you use as well, that makes it sound like an afterthought to me, if only because as well as is not a true paratactic conjunction; that is, as well normally does not introduce a true clause with its own finite verb, but a phrase of sorts. For that reason, the as well... phrase is not a true elliptical clause, but something else, like an adverbial phrase or an afterthought, deserving of its comma.
I agree with Edwin above that your second example is infelicitous, because it is a little bit difficult to parse, and the enumeration is possibly even slightly ambiguous.