Cost, mostly. Plus the in-setting version of cyber-phobes.
Like, it gets glossed over in a *lot* of media/games, etc, but the relevant cyber-ware and attendant therapy *cost*. Even in GitS, full conversions are rare, hilariously expensive, and tend to be NDA'd out the ass. Like the Major says, their bodies and memories aren't theirs. And she's top-secret elite government black-ops. Joe Wageslave and Cindy Ganger aren't anywhere *near* that tax bracket. Any cyber they end up with comes with (successful) crime or is of the "we removed your need to eat so that you can convert time units to code lines more efficiently, no that doesn't come with a pay raise and isn't optional" (outside of a blunt force game balance tool, that's what the humanity stat is supposed to represent, not uncoerced wanted upgrades)
Being trans in Cyberpunk is like being trans now, just faster and with a slightly better chance of "passing"