Beta testers are free to use the sim as they like, but of course when reporting issues you need to rule out impact of mods just like you would/should do before reporting in the public forums.
Since mods might be incompatible with the update in test, you rather reduce the set of your addons to the minimum anyway.
The issue are not the tests, the issue is how much time and priority you have to fix the found issues. And with a marketed XBox release, there was simply not much room even if you have a 5 week beta period.
But I’d like to emphasize again:
As with every beta test, you cannot judge from the final release in how far the beta period was useful since in the best case scenario, the critical issues found during beta are fixed in before/in the final release.
Having the most realistic setup with mods and addons will give you a much broader picture. Also remember that sometimes if a 3rd party addon shows issues, it still might be down to a bug in the sim. Not all of the sim is using the full SDK itself, some features are mainly provided for and used by 3rd parties but the features/API is still part of the sim and worth to be tested.
P.S.: The above said is all general to the beta testing approach. I try to avoid talking about anything from the contents of the test to not violate the NDA. Hope you understand