Transit costs are a small fraction of "construction". I agree our transit development costs are insane though this has a lot more to do with America's very strong concept of property rights (and the weaponization of other apparatus to defend property rights) than simply "red tape." I.e. it's more political than bureaucratic.
No it doesn't. Any publicly funded construction is rife with tons of additional regulations designed to limit (but sometimes perpetuating) corrupt contracting, and transit projects in particular have very unique needs around land acquisition.
Even still, the linked website doesn't really seem to say permitting is a major driver. And it certainly doesn't dwarf labor and materials.