Hi Shawn,
I have been using FP since back in the 90s, and have never had it affect any of my cgi or php scripts. The only thing I have noticed it does, and it ALWAYS does it, is it puts those _vti_cnf files in every directory, including the scripts directories, but it doesn't bother the scripts.
One thing I would suggest is to not work on the site offline (on your computer) then “publish” it, work on it online (on the server), and then “save” pages as you change them. It is much faster, and it doesn't affect any other directories/scripts, except the one you are working in. If you work offline, and then "publish," it has to go through EVERY directory and file, comparing times/dates/sizes to see what has been changed, what is new, or what has been deleted. And, it puts those _vti_ files everywhere to help it next time in this process.
Again, working on the site online; http://www.yourdomain.com is just like working on your computer, and you just hit save when finished. No mucking around in the other directories and/or scripts.
The downside, you only have one copy of your site that way, and that is the one online. But, about once a week or so, I "publish" the online site over to my computer to have a backup offline.
The downside of that, if you want to see it as a downside, is that it will bring your php and cgi scripts over to your computer when it publishes to offline.
Still though, it is faster and less hassle to just do the work online. I discovered this out of necessity, my main site is over 9000 pages, all created in FP, and making one change on one page and then publish... the publish took sometimes 10 - 15 minutes for FP to do all that comparing of dates, etc., and just wasn't feasible for one simple change.