There are slight differences. The Mk1 and Mk2 amps were small batches,
only a few hundred made, the Mk3 has an extra pre-amp tube, PCB,
cheaper transformers and chasis, and some minor aesthetic changes (thicker wood frame, vents, etc).
Planet of the amps
did a piece on the Mk3. They found the cheaper transformers limited the output to 160 watts and the pots they used limited the EQ range. I've never personally compared the two, or a Mk3 with changed pots, so I can't say how much difference that makes.
As far as PCB vs point-to-point, given the same circuit layout/components/etc, there should be no difference between the two.