Many years ago (when nmh was mh and back before MIME was a thing and attachments were rare, so command line stuff was able to do 100% of my email handling) I simply had two accounts on my UNIX system. One for me and one for my alternate ID. There was some extra work involved keeping things straight and/or tweaking configurations when I pushed out a configuration change (say, more headers to hide), but it was minimal. The biggest "gotcha" was the mental footwork to keep contexts separate (start dealing with email in window 1 as me, get distracted, switch to window 2/alt ID...). I technically had 3 such IDs (work at $employer, two personal), but the work/non-work separation was physical (and ~1000 miles) while the other two involved the same data store and infrastructure.
Using different UNIX accounts ensures 100% separation. You can do everything under one ID in theory, but you'll spend a lot of effort/time switching email IDs via different profiles. My opinion is that this will be error prone unless one has a lot of self discipline.