I've been gradually transitioning to the "Gensoukyou" spelling in my own use, since it was the one we went with for EoSD New Classic and I feel like at least I have to commit. Having to choose between two kinds of consistency, I've decided to keep the Gensokyo spelling in all the ongoing series and switch to Gensoukyou in any new and future ones, even though this means having both in use at the same time.