Thanks for the clarification of your setup, and yes I understand how yours is set up now - with three WP sites in total. Obviously with that scenario, each of your WP sites will have its own .htaccess file in its own respective directory, and your "WordPress Address (URL)" will always be the same as your "Site Address (URL)".
So this is still a different scenario than what I have, whereby my WordPress Address and Site Address are different from each other - so WordPress is running from the site's root URL, but is installed into a subdirectory.
In my scenario, the .htaccess file goes in the root directory, when WP is installed into a subdirectory. This is also described and confirmed at http://codex.wordpress.org/Giving_WordPress_Its_Own_Directory.
I also disagree with your statement that "WP had no bearing whatsoever on where the htaccess is" - this is not correct. In my setup, with the WP files installed into the subdirectory, WP itself will still update the .htaccess file in the *ROOT* directory. I'm not referring to a plugin, but WP core itself. It does this, for example, when you go to the Permalinks page and click Save Changes - WP itself (not a plugin) will then add its own section to the .htaccess file, and it uses the copy in the ROOT directory, even though it's installed in the subdirectory - it's clever enough to do that.
In fact, you can completely delete the .htaccess file in the subdirectory - it's not needed, and WP core will never use it or write to it. It will only write to the copy in the root dir.
BWPS, however, isn't so clever. Even when there is no .htaccess file at all in the subdirectory, BWPS will simply create a new file there and write its stuff to that one, rather than using the already-existing .htaccess file in the root directory, which WP Core is writing to. And that's the crux of the matter - I believe BWPS shouldn't do that. WP Core is somehow able to "know" that it's running out of a subdirectory install, and BWPS should be able to figure that out too.