Rather than copying the entire TA and making modifications to multiple copies of the TA (and keeping both updated with new releases etc.), I'd rather suggest to install the TA just as is, without any active inputs.conf. And create separate small apps that contain the inputs.conf that you need.
When deploying on universal forwarders, I think you don't even need the TA itself at all on the forwarders?
yes, yoo can create two TAs, called e.g. TA_Windows_all and TA_Windows_perfmon, copying the same TA_Windows and customizing each one for your needs.
After you need to create two different ServerClasses for your systems putting the correct servers in each one.