Theres a reason why maya has a usersetup. mel and whyy its different for every user.
If you for some reason must share thees ethings then Make sure you either build a mechanism for everyoine to have tehir own customisatioos.
What i would do is either a)
mekse sure everything your sitewide is sourced somewhere else, that still gets sourced by maya thats shared for everyone ad let the usersetup actualy be users usersetup. (theres a reason why maya has a folder scripts folder in ist root menu just confgure maya away form them and you have userlayer and nonuserlayer separated)
OR the stupidway
let the usersetup wich noe is a globalsetup, wich ist shouldnt be call a catchQuiet source to a file called trueUserSetup forexample and make sure theres no such thing in the repository and if such exists in the users or the prohects path it will then be run.
But ime pretty sure no one at your place actualy tought of user cutomization whan they did the system. Wich means you realy need a mel expert out there.