wordpress won’t touch your templates, unless you use the built-in web-based edit feature, and if you do, its your own damned fault.
… edit the files offline, and upload them by FTP – if you do this, wordpress won’t ever save over them.
Others on the site use wordpress’s built-in system, I do not. Regardless wordpress should not constantly increase the size of it’s templates for no reason, it should do the opposite.
My caching system must have rules prior to wordpress’s, and I doubt having rewriteengine on called twice is a good idea?