Dinking w/ Mail after posting above -- I'm now using an old-school work-around that will at least keep me from replying to the wrong person in a mixed thread. I'm sure those of your more familiar w/ Mail are ahead of me on this, but in case it helps someone:
First, in the Mail app, uncheck "Organize by Conversation" under the View menu. Now all of your emails are no longer grouped by thread.
In any given email, hover over the email addy/name and you'll see a little caron ( ˇ ) to the right. Click there & you'll get "Search for..." at the bottom of the pop-up menu. Give a click, and the emails from that person come up. It's not neatly threaded & you may have to open multiple emails instead of scrolling, but at least the list is sortable by subject & not mixed with unrelated emails.
Yeah, lots of steps for what should be automatic. But it'll keep me from mixing important emails until a fix shows up or I find better software.