.htaccess files are not exclusive to WordPress. http://en.wikipedia.org/wiki/Htaccess
FYI - the disadvantages performance loss info on that Wiki page is incorrect. .htaccess files do not cause a performance loss and whether or not the httpd.conf or the .htaccess file contain the rules it does not make any difference - there is no performance loss when using .htaccess files. Thousands of lines of .htaccess code can be processed in milliseconds. ;)
"...apart from 1 where the blog was installed in sub-directory and was a small part of a larger PHP driven e-commerce site..."
If you put an .htaccess file in a folder then all the files in that folder will follow the security rules in that .htaccess file.
If your other php application or platform requires it's own specific .htaccess rules then you can create those using the BPS built-in .htaccess File Editor. Usually a good site architecture will keep separate apps in separate folder as sharing folders can be problematic when trying to apply website security to each different app. And in general you should have all apps in self contained environments / directories / folders.
If a Parent folder has an .htaccess file created in it then the subfolders of that parent will also have the .htaccess security rules applied to them.
If you add an .htaccess file in a Child folder of a Parent folder then the Child folder will follow the security rules of it's own .htaccess file instead of the Parent .htaccess file.
When you use AutoMagic to create your Master .htacess files and then Activate them with BulletProof Modes. The Master files are copied to the respective folders for that site ONLY >>> 1 .htaccess file is copied to the Root folder for that site and 1 .htaccess file is copied to the /wp-admin folder for that site. The Deny All .htaccess files protect BPS files themselves and are copied to BPS Plugin folders.