From what I understand, both Octoprint and FreeLSS are applications that run on ARM-based Linux distros.
So in theory it should be possible to run both, yes, but I am not experienced enough with Linux to say for sure. OctoPi is just an SD card image that has Octoprint already pre-loaded and configured for a RaspberryPi, but it's not necessary to use that image to run it on a Pi. (Same goes for the pre-formatted SD card that comes with your backer Kit (if you are a backer), it's not the only way to setup FreeLSS).
The only issue really would be performing a scan WHILE also controlling a printer, especially if you are controlling it through USB, and even monitoring it through a webcam. That's both a lot of USB cables coming out of the Raspberry Pi on your Atlas as well as taxing if you do too many things at once, especially if you don't have a Pi2.
Someone far more knowledgeable about Linux can probably give you more detailed advice, but as for it being possible, yes, it most certainly is. Just how feasible it is with all the extra cabling (not to mention having to use your Atlas as your main control center/computer for all your printers) and how much of an impact it will have on it's memory or processing is something I have no idea of.
Also, not sure how much power the Pi gets with Atlas's setup. The Previous Raspberry Pi was fine with a 1Amp power adapter, and while the Pi2 will be fine with a 1Amp as well, it's recommended to use 2.5Amps if you are going to use a lot of USB devices. Plus the Pi on the Atlas is NOT powered through the MicroUSB port like most RaspberryPi setups are.