No, they will only run from AmiBench at the present moment.
The correct answer is YES :-) But they need access to various libraries in SystemV46, so when setting up your 3rd party OS install, tick the include global systemv46 check box. SystemV46 has boot priority of 0 so make sure your boot partition for your OS install has a priority of 1 or greater.
Then do:
Assign LIBS: SystenV46 ADD
either just before you launch the application or perhaps in your S:Startup-Sequance, making sure it's after any LIBS: additions you need for your own OS's needs.
I've been meaning to try and demonstrate this in a video but time is scarce.