What I meant is that, if he's controlling like that in the manga (where he also isn't working alone, you know), I really don't see him not being so in one of the games, of all things.
The Myouren Temple can probably just turn back into the ship (the wiki says it can, although it doesn't give the source for that claim), and none of the youkai of the surface that canonically go underground during this game (as in, go there during their story modes) were originally from Gensokyo (in fact, Ichirin was living there before UFO), so I'd assume that the deal doesn't apply to them. Alternatively, no one down there cares about this rule anymore ever since the events of SA (consider that underground youkai were also forbidden from going to the surface, yet Orin does so regularly now, and Yamame did it at least once, to visit the Myouren Temple).