I really disagree with your statements in that bug comment that it's a hardware issue, and that it's not fixable. I've been able to easily reproduce it with two different iphones, one of which I had a 6 month history of syncing with media monkey successfully before upgrading to ios8.3. So it's definitely something that's changed in the OS between 8.2 and 8.3 which is causing this, not hardware.
The other evidence that it should be fixable is that it's easily reproducible with media monkey, but does not ever occur with iTunes. This suggests that MM is doing something different in the sync protocol than iTunes does, and that difference is what triggers the iPhone to reboot. It may be difficult to determine what that difference is, but it must exist and figuring it out is the key to fixing this. Given the difficulty you've had in tracking it down, and the impact that auto-conversion seems to have on the bug, my money is on a timing related race condition.
Please note that up thread I disproved the notion that small batches was a viable workaround for this issue, I've seen it recur with a batch as small as 150 songs. Certainly it's less likely to occur with a small batch, but that's expected behaviour for a heisenbug like this -- the longer the experiment, the more likely it is to occur during the run.