Actually, setting junction points would be of no use to me.
All programs that I deem system-critical (Such as NVIDIA Geforce, Anti-Virus, etc) are located on my system drive (I.E %ProgramFiles%), but the rest are scattered on my different drives.
I ended up writing my own program to rewrite some of the sections in the winapp2.ini file, based on installation data (Registry, WMI, etc).
So, instead of using environmental variables, it uses absolute paths based on my own system.