Maschi, you can install oMega Commander and have any number of portable instances and they should not conflict.
There is though couple moments you should be careful about.
If you define the same hot key to switch to the application, currently open instances may compete for it and any of them will be activated.
Also importing/exporting settings with specific paths may have some side effects, which can make your portable instance not as portable. Stuff like that…
The Pylonos Team.