"t's when I stop sixaxis and it restores my bluetooth (or says it does... or gets stuck and never says it does) my bluetooth simply can't be switched back on until after I reboot..."
Obviously, its at the fault of the app, because otherwise (sixaxis not installed/used) bluetooth would function properly and no restart would be required.
Therefore, sixaxis is not ending support of the controller properly, re-enabling bluetooth support, or whatever its trying to do for the device, android version, or whatever its problem is in code.
Probably good to let the app's dev know about it and find out if they say anything.
Since root access is required, it definitely requires some deeper access to android (the deeper the more problems are likely to occur). Some code doesn't even work for all devices and they could have gone that route with their app knowingly - whether it was a necessary side effect due to the type of app they created or specifically because of a workaround of what google allows devs to do with android.
Either way it is often an app with problems as reviews show.
Moto G 4G | latest official rom 4.4.4NEW (Longest recorded uptime: 503 hours with 4.4.3)
Nook HD+ 32 | cm11 emmc official rom (331 hours is about the most I can get before forced reboot or other.)