A colon or a comma in alternative questions

That's possibly because both are reasonably legible to most English speakers. In other words, whatever you prefer!

To expand on that ...

In the context you've given - a choice of two things - either works: it really doesn't matter.

If you had more than two choices - say apples, pears and bananas - it really needs the colon to be idiomatic; and if any of your options has a conjunction in (for example: Which would you prefer: strawberries and cream; apples and cinnamon; or prunes and custard?) you should use semicolons rather than commas to separate the list items, so that there is no ambiguity (otherwise it's conceivable that somebody will misunderstand that each option is a pair of things).

In speaking, of course, you can't see the semicolons, so you have to pause slightly longer, and be sure not to pause during each item ;o)

Also, some people - myself included - will tap on a finger for each option, as if counting them. This non-verbal part to the communication helps to distinguish the items even if each is a compound thing.

EDIT: a couple of pages found in moments with a quick search via Google ...

A page on “The semicolon” from an “Improve Your Writing” grammar tutorial hosted by U. of Bristol shows use of the semicolon where list items themselves contain a comma, which isn't the problem here of course, and contains the wonderful phrase “In a situation such as this, only the mighty semicolon can unravel the mess.” They don't include the conjunction, but ...

... this page, a “Grammar guide” on “Using the semi-colon and colon” (sic) hosted by U. of Leicester does contain multiple list examples all containing a conjunction after the final semicolon ... because where else would you put it?