Hi Banani,
As far as I am aware, I don't think it is possible to be use more than one version of custom-variables.js file as of now.
If you want to use different styles for different deployment packages then I think you have to create multiple theme zip files and select the required one and commit before creating deployment package.
There are multiple app store widgets allthough currently not yet for Mx 8 but you could give them a try to see if they still work: https://appstore.home.mendix.com/link/app/108878/JAM-IT/Reconfigure-Stylesheet
https://appstore.home.mendix.com/link/app/106033/TimeSeries/StyleSheetSwitcher
Regards,
Ronald