Yes, what BPS is doing is very complicated and the code is very complex, but the user end of it has been very simplified so that users only need to click buttons without knowing anything about anything.
"...what is the equivalent less intrusive alternative?"
The answer is none. I'm pretty sure that BPS has the most extensive and comprehensive .htaccess code of any htaccess security plugins or security plugins that use htaccess security code. The help and messaging is very simple, clear, easy to understand and leaves the end user with simple "click heres". It doesn't get any simpler than BPS.
"intrusive" is an incorrect adjective to describe BPS. I think you meant to say less extensive or less comprehensive or maybe just more simplied. BPS looks/checks much deeper than just the surface level and displays and provides extensive help information. It may appear overwhelming at first, but my personal opinion is that "too much help information" is always better than "not enough help information".
Please read the entire displayed help message that BPS is displaying to you. It explains exactly what needs to be done and provides a link to the W3TC settings page in the displayed message. Click the link in the displayed message, do what the displayed help message says to do: click the W3TC auto-install or deploy buttons as explained in the BPS displayed message/alert.
NOTE: If your root .htaccess file is locked then you need to unlock it first, by clicking the Unlock htaccess File button on the BPS Edit/Upload/Download page to allow W3TC to write to the root .htaccess file. This information is also displayed to you in the BPS message/alert:
"...If your root .htaccess file is locked then you need to unlock it to allow W3TC to write its htaccess code to your root htaccess file."
The entire displayed message/alert:
W3 Total Cache is activated, but W3TC .htaccess code was NOT found in your root .htaccess file. W3TC needs to be redeployed by clicking either the auto-install or deploy buttons. If your root .htaccess file is locked then you need to unlock it to allow W3TC to write its htaccess code to your root htaccess file. Click to Redeploy W3TC.
NOTE: The Blue Read Me help buttons throughout BPS provide extensive help information.
The BulletProof Security Forum provides additional help information and troubleshooting help: http://forum.ait-pro.com/forums/forum/bulletproof-security-free/