suExec questions

[P15-D24]

Site is IPS 4.X, Apache on Ubuntu. Site has been running for decades, literally, with upgrade ongoing. Been dealing with an ongoing issue where 3rd party add ons often get uploaded as nobody owner, then when I try to run the installer get errors like the dir is not writable  (even if set to 777) or you don't have access. In talking to my ISP their standard approach to this issues to run PHP as cgi under suExec.  It turned into a disaster and I'm trying to understand why.  First, a disclaimer, this stuff is way above my pay grade so if you can keep it simple.  Steps taken were first to update ownership on the nobody files to my site username, probably about 200 files mostly in the /applications. Looking back I forgot to do a quick touch test to see if this broke anything on the main site, but did a touch test in Admin and some of my installer issues were gone and everything else seemed ok. Then they did the rest of the server config change for suExec and touch test on Admin (OK) and the main site. Well the home page loaded but every link was broke with a can't find the URL error.  Could not access anything. Ended up doing a restore from backup for my site files, and everything started working again for a while, then the CSS files stopped loading with a can't find CSS file errors.  So we did a second restore and turned off suExec and everything is working again, but I have the original issue back with installing 3rd party packages. 😞   Down all day, and not sure what to do next. Comments, explanations and suggestions for best way forward welcome.