The reason it's not recommended that you remove (and or replace) the box leaving the TC attached to the driveplate is that there are seals on the main shaft that can be damaged - obviously fluid flows and returns to the TC via passageways in the main shaft assembly. The seal on the gearbox front cover only prevents fluid leaking from the box.
If those seals get damaged you'll end up with little or no pressure and the box won't operate. They usually need the box to be stripped to replace.