This が is not a replacement of か. You cannot use か in the first place; ポテトかサラダがつきますか ("Does it come with either fries or salad?") doesn't make sense as a question from the clerk.
This が is the が which you probably remember as "but". In this sentence, が is there to provide background information, and the actual question (どちらにしますか, "Which do you like?") has been omitted.
Okay. It comes with fries or salad, so...(which do you like?)
In Japanese, it's common to omit the final part of a sentence if it can be inferred. If a sentence ends with "が?" or "けど?", something like "what do you say/think?" or "what does it matter?" is often the omitted question. Similar examples:
But it's Sunday tomorrow, are you sure?
Yes, I can speak French, but why do you ask?