I regularly install to program files, and change settings and meddle with files all the time. No issues, not with EB1 or any of the other hundred games there.

As for XSamartan, to cater for people who install somewhere else just allow them to target the folder of their choice with the installer. I fail to see how thats difficult or a strange thing to do, its been done for as long as I've been gaming back in my old Win95 days.

I don't mean to trivialise your work by any means. I am sure it requires quite a bit of effort to set this all up (and I wouldn't know how to do it) but you write the list as if its things that are uncommon or likely to be missed during design when they seem (mostly) self-evident.