Ok so I've done an investigation, and the issue (I think) is the plate between the engine and the gearbox. When the starter motor is removed, the engine then turns by hand. I think the plate itself slipped down, so it's pushing the starter motor down on to the flywheel as there is witness marks on the tip of the starter motor where it's hitting the flywheel.
I've removed the bolts from the gearbox and separated them to try and move the plate with no luck. So I can either drop the gearbox, take the clutch off, and the flywheel, to then unscrew this plate and move it and then see if I've done it right by putting it all back together again. Or, I can dremmel the bit of the plate that's preventing the starter motor from sitting properly, move it up and attach it using the RTV gasket stuff I used for the oil sump so I still maintain the gap between the motor and the gearbox.
Don't think it'd surprise anyone if I say I'm going to try the latter option tomorrow. But yeah, it's how the starter is fitting to the gearbox which is seizing the engine, so this will at least mean the car can start.