The 2 locating dowels for the gearbox alignment with the engine and crankshaft are supposed to be in the "rear engine plate" not the flywheel
And they weren't actually dowels on at least some TR6 (all I think). Instead, there are two special tight tolerance holes, and the factory used tight tolerance bolts (what they called "dowel bolts", PN 132872) in those holes.
Having the pressure plate out of line would just cause vibration, I think. More of an annoyance really, although it might shorten the life of some components around it (like the rear main and transmission input bearings).
But I suspect that having the gearbox out of alignment with the crankshaft (because someone left those bolts out or used ordinary undersize bolts in their place) is one of the causes for the infamous TR6 clutch problems; and can also cause problems inside the gearbox. The input shaft is forced to run at an angle to the other shafts, which in turn forces the center of the clutch plate to run at an angle and the clutch to drag. Might even be the reason for a weird clutch failure that several local club members have seen, where the flat metal plates that connect the friction surface to the hub break and tear.
When I got Stag #1, those bolts were missing, and it had a bad bearing between the input and mainshafts inside the gearbox. Not a common failure mode. I paid a professional to change the gearbox & clutch; he still left them out and several others besides. (That shop is long gone now.) After I fabricated and installed the dowel bolts (along with replacing the broken flywheel housing), the clutch worked better than it had since I bought the car.
No one seemed to have the right bolts for the Stag (although a few vendors sell ordinary bolts as replacements), so I bought some drill rod in the right size (3/8" IIRC) and threaded it on both ends for nuts. Another alternative might be to buy aircraft bolts with precision shanks, but I wasn't able to find them at a reasonable price.