John,
Those pins should work great for keeping the motor in exactly one place, speeding alignment at maintenance time.
I thought about the pins, too. However, based on both theory and testing by others, the mount seemed adequate as-is for my purposes. Others pointed out that many ARFs use similar "clamp only" designs. Plus, I'm looking forward to testing the effect of rotating the engine for up/down thrust as part of my ongoing efforts at tuning and trimming.
No real problems with handling the engine on test flights last night, except that I ended up using a longer NV, as the short one hit the mount's clamp bar.
Peter