The military wouldn't use a TF-22 trainer because a cheaper alternative is already available in the T-38. But the T-38 is cheaper because it is a smaller, older aircraft built using Vietnam War era technology. the T-38 is still an effective trainer however because if you look past all the stealth and fancy computer systems on an F-22 its still just move a stick and the plane pitches, yaws, rolls and accelerates; just like the T-38.
On a VF-1 however there is no equivalent already in existence. There are no pre existing production aircraft that can turn into a Giant fighting robot which you can use as a trainer. You’re going to need something to train people on how to operate those alternate modes, and the cheapest way to do that is to modify the VF-1 (the only variable plane available.)
Once they went on to newer VF's like the VF-4 or the VF-11 they were probably still using VT-1's for training purposes as those are fine for teaching the basics of Gerwalk and Batroid piloting.