I wrestled with this for a while. I reported it to ASA, but it never got fixed. It is another example of ASA software that is broken and it is very frustrating. They have fixed other issues I have identified in their software, so I am unclear as to why they focus on some and not others.
My solution was, like yours, to control the dome synchronization using other software.
To address the timing issue, in Sequence, I set a mount settle time that is long enough to allow the longest slew required by autopoint during a model build. That adds a lot of time to the model build, but since I do those infrequently, it is a workaround that I can live with.
There is a better solution - a fellow ASA user has built a NINA plug in that will do autopoints job, and NINA controls the dome correctly.