The special bolt which holds the starter motor in doesn't serm to extent very far through the engine case.

It doesn't look as though it has been shortened, do they come in different lengths?

All 110mm is it engaging in the v on the starter

Any bolt will do. It`s not essential to use a shouldered version as the one in the photo. Ordinary bolt just needs grinding to make the flat and reduce "head height". Bolt protrudes just sufficiently to get washer and standard nut on.

More likely that an aftermarket starter has a thicker flange than standard 

Sorted.
I was trying to get a nylock nut on. Got a standard one and it fits just fine.
Might not have been sitting in the "v" also.

Thanks all for your input.

Ah.... Been there, done that. Nyloc nut does go on but rule of thumb is two threads minimum showing thro nyloc nut. You can get "low height" nyloc nuts but I have not tried them on this bolt.

Better off with normal nuts in awkward places as once loose they sometimes undo with the fingers rather than spanner off until the nylock is clear.

Agree with snoopy here. Nylocs can be a pain to remove when in a seriously awkward place.