Thanks for the reply. The intention is to not have BPS warnings displayed in WP-admin dashboard unless something unexpected has happened. Manually editing the .htaccess file had the result of triggering these warnings (as appropriate).
I'll give a go to the editing of the master .htaccess file, and if it works, in other words, if that's what BPS compares the active .htaccess file to before deciding whether to throw a warning or not, we'll likely set up a cron script to periodically check the .htaccess and master file and modify them as warranted. This'll let us see the BPS warnings if something unexpected happens, and doesn't depend on plugin updates.
A less hackish solution would be if BPS offered the possibility to turn certain features on or off. There are several other user-agents, such as libwww-perl, that webmaster might want to enable temporarily or permanently. Having a GUI for this would be useful.
Thanks for the offer of creating a custom code snippet for us. The application is still under heavy development, so the query vars and so forth will change so fast that I don't want to task you with this, at least until the main development effort is behind us.