The mounting flange is only thicker on the later gearboxes; and the extra thickness is to the rear. In other words, the face of the flange stays the same distance from the clutch shaft, and you can continue using all of the TR3 clutch components if you choose.
I did that for several years with my later TR6 gearbox housing, and it worked out fine. The only issue is that the thicker flange moves the slave closer to the lever, so if you use a gearbox with the thicker flange, you will need to either change the way the slave mounts; or shorten the pushrod. I shortened the pushrod.
If you do want to use the later clutch, you'll have to either replace your flywheel, or have it redrilled and tapped. (The drilling is a precision operation, you'll get bad vibration if it is done wrong.) You'll also need the carrier and throwout bearing to match. My alloy flywheel was only drilled for the later clutch (and the later clutch is smaller and lighter anyway), so that's the setup I use now. But the slave problem remains the same (and I'm still using that shortened pushrod).
PS, one other consideration: If you switch to the later clutch but get a TR3-4 gearbox, then the front cover on the gearbox has to be shortened. But using a TR3-4A gearbox solves the slave problem, as they have the thin flange. (Not certain offhand about TR250 and early TR6, but I think they were thicker than TR2-4A, just not as thick as the later TR6 ones.)