Question followed by an explanation/clarification of the question

If you use actual parentheses, the use of the question mark becomes apparent:

Would you like to eat an apple?
Would you like to eat an apple (which is a kind of round fruit)?

The same is true of the nonessential, appositive information provided in the question after the comma:

Would you prefer that or the status quo?
Would you prefer that or the status quo, which is . . .?

But as with anything that looks strange, even if it's correct, it may not be useful to keep it phrased as it's been written.

For instance, the sentence could be rephrased:

This is x. The status quo is y. Which would you prefer?
Knowing that the status quo is x, which would you prefer?

You could use actual or a dash:

Would you prefer that or the status quo (which is x)?
Would you prefer that or the status quo—which is x?

Or it could be broken into two parts:

Would you prefer that or the status quo? (The status quo is x.)

Last, depending on the nature of the missing information from the question, it could be used adjectivally:

Would you prefer that or the x status quo?