You can make a second "user directory" called TFTDuser, and have a shortcut which has argument -user TFTDuser
After that, the configurations are completely separate.
Or You can duplicate the installations :
- Have one openxcom installation, with a "user" subdirectory, UFO files, set up to run UFO
- Have another openxcom installation, with a "user" subdirectory, TFTD files, set up to run TFTD
The "user" subdirectories ensure that each installation is completely standalone.