When you think about it this doesn't seem to an inherent problem in Stellaris. For example, pop evaluation on each planet could be done in parallel. In most (if not all) scenarios there's no contention for any data at all.
I agree. The parallelisation of many functions could be improved. However, refer to an earlier post where I talked about engine updating and business realities. There's only so far @Moah and co. can get under the bonnet, before they're likely treading on the toes of the team doubtless working on ClauseWitz2whatever.
I doubt he can comment, but I pinged Moah to see if he wanted to clarify regarding this.