Yes, focus breathing will always be an issue, but my experience is HF seems to do a good job in handling it.
If one of the three methods in HF doesn’t work, I try one of the other two. If I’m still not happy, like you, I’ll go to PS, or try one of my other stacking pieces of software, eg Zerene.
BTW just added an additional user feedback item, ie estimated number of brackets so the user can interrupt the script if they believe it is too high.
The M3 Brackets scripts is not the fastest script, but it does the job for me, ie ‘perfect’ deep focus stacks, plus exposure bracketing, on an M3, for scape photography, ie on a tripod and when we are also slowing down to enjoy the scenery ;-)