I can see how it would catch you off guard if you were using RTH or FLY to land and it suddenly switched to Fly:Manual, but if you're fully controlling it anyway, then there should be no surprises, even with GPS loss.
Tom,
We have differing opinions. If your bird is two feet off of your landing zone in a 10-20mph wind and you lose GPS, it'll tighten up your sphincter! Especially if experience with fly:manual is limited. Just my opinion, of course.

Jerry