If it is so easy to program a fully functioning ATC system that can deal with correct and incorrect flight planning, real Wx, terrain etc…why don’t you program something and sell it as an add on ??
I tried to give you one “workaround” to deal with some of the JoJo commands one can get from the canned ATC. Does it work 100% of the time ?? No it certainly doesn’t because the canned ATC has quite a few things that need fixing.
In this particular case it probably would not, and once you are cleared to leave the planned cruise altitude it usually doesn’t make sense any more to ask for something different or you don’t even get that option anymore.
The approach phase is for me the one that should be “easiest” to get better using published procedures. But by no means easy.
I have flown into Eureka a few times IRL and the terrain east of the airport qualifies as mountainous I would say and definitely rugged. The variations you saw at the end could be due to the different MSA altitudes around the airport, depending on which approach you had.