I will at some point add the additional coding functions that will detect whether or not it is a WordPress network installation / MU installation and all the other aspects of Network / MU sites and automate everything. This is a very simple and easy thing to code, but time consuming like all coding is. ;) I just have not gotten around to writing that code yet because it had very low priority in the overall BPS growth and priorities list. It was decided very early on that if someone had a network installation / MU site(s) then their level of WordPress expertise would most likely be a bit more advanced then someone brand new to WordPress with very little experience. You have a very valid point in regards to how htaccess should handle multiple sites from a central location without actually stating that. htaccess in general is a very grey area to most people. When you google information regarding htaccess coding you will find a lot of bits and pieces of a much larger puzzle and if you understand the info well enough you can assemble the bits and pieces together to create comprehensive and logical htaccess solutions (and some really cool and fun stuff with htaccess too).
In regards to the admin screen issue i am unclear about what you mean exactly. Network / MU sites have had very little attention and focus because this area has not been prioritized for the reason i stated above. I can put you in touch with an Network / MU expert (Scott) that has contributed to BPS regarding what Network / MU site setup entails. There is also info in the BPS guide that Scott contributed regarding Network / MU sites. And this below is one of his statements regarding Network / MU sites.
“…for a subdomain install. I did just a normal Activate (not Network Activate) which seemed appropriate since there is only one root (and one root .htaccess). I verified (after making the change I mentioned above) that both the main blog and another subdomain blog were protected against your example search hack. I don’t think a subfolder MU setup would be any different, but haven’t verified that….”
Regarding this statement you made...
"Like I said, it's not going to find any actual folders of the subsites when a user is going to use the plugin in a subsite."
Depending on how things were set up this may be true. I would have to defer to Scott's expertise in this area because quite frankly I have spent very little time looking at Network / MU site requirements.
BPS is currently designed with a single site focus and htaccess in general is intended to be used in a literal way for specific domains / directories, but can also be coded / modified / used as and in a central / root location and way so that multiple sites can all be "controlled" from one central domain or root directory.