The launchers (KSM6 and AdvBoot) have more impact on the stock code (and that is minor and restricted to a single startup script), than Koreader which makes no changes to the stock code. It does make some use of the stock routines, so the Kobo firmware can impact koreader, koreader doesn't impact the Kobo firmware.
The current Koreader build should run, no matter what firmware is installed. Any lack of performance or function resulting from a version incompatibility would be restricted to the functions Koreader uses/calls from the Kobo firmware, (like sleep, frontlight, Wifi, ect...). In other words, Koreader should run fine, except that such a function may not work properly, all the rest should be ok. The GitHub Koreader team has been very quick at addressing any such problems.
The device specific problems, when they arise, are often the hardest to track down. I am not sure if there are any such still being addressed for the Aura 6". You might check at
the project pulse page
. And click on Issues.
Luck;
Ken