That is the way the flaps on my RV-6 are wired, straight to the battery via an in-line fuse
at the battery.
The reason I wanted the flaps always hot was for convenience, not a "fail-safe" reason. I like being able to lower and raise the flaps without the master being on. This comes in handy in the hangar during cleaning, and makes it easier to raise the flaps prior to engine start before the master is switched on.
This is strictly a personal preference deal, do whichever you think will work best for you. As long as you fuse the flap power lead, I can't see any reasons for not having "hot" flaps. I guess a stuck switch might be an issue, but the flap motor will run with no harm when it hits the end of the travel, and what are the odds a flap switch will fail closed while the plane is sitting in the hangar?