I've done it a few times, and it worked perfectly well each time. Here [0] for instance, a couple repos had evolved to be codependent, and so we combined them into one.

But it's something that you only have to do rarely. Projects merging is far from the normal PR after all, and it makes sense to give a warning in such a situation.

0: https://github.com/replicatedhq/kots/pull/511