-There is no weakness if the ability to manipulate boundaries. However, nothing can beat Reimu's Fantasy Heaven/Nature.
I personally favour the opposite: there are weaknesses in the ability (at least in a practical sense), mostly stemming from Yukari having neither infinite energy (explaining why she couldn't use a regular gap to the moon, and had to use a more esoteric method) nor infinite calculating ability (although admittedly the latter is ridiculously high, according to Ran). Meanwhile, boundary manipulation is a natural counter to Reimu's fantasy heaven, simply by shifting the border of existence and its negation such that Reimu is back on the "existing" side.
I also like the idea that humans don't normally have much magic potential, even in Gensokyo: Reimu does, being a shrine maiden and having high spiritual power, and Sanae does for similar reasons. Marisa uses her magic through catalysts such as the Hakkero, her mushrooms, and explosive potions. There's enough magic in the air that anyone with the capacity to manipulate it can fly by moving the energy around themselves to create thrust or lift.
It doesn't mean much in pure-Touhou stories, but I also favour the idea of the hourai elixir removing the concept of death from the drinker, and thus being meaningless against any weapon, magic or what-have-you that functions by introducing a concept of death or mortality rather than acting on it (so the Nasuverse's black barrel could kill Mokou or Kaguya, but the mystic eyes of death perception wouldn't see anything to cut).
