I was investigating the issue and noticed after I profiled b3 last time, I turned off various PostProcessScene steps in the project, to check if it affects the “Destroying a Prefab…” error and I didn’t turn those on again.
Sooo… the huge performance drop from my previous b6 profiling session can be seen as wrong data, because it was measuring the performance without any optimization steps, thus significantly slower than before and not a meaningful comparison to earlier profiling results.
However, since PostProcessScene causes some issues here , I ran those optimization steps outside “build player” to have the proper optimized scenes and then did a build afterwards.
The results are much more like Unity 2018.2 now, see below. 2018.3 is still slower than 2018.1 with my project though.