It's just a matter of becoming familiar with it. Windows wasn't easy coming from Mac years ago. Now I have Windows 7 and latest MacOS in the house to try to comprehend. I think your choice of naked Android (Google product) may help in many regards because your tablet isn't loaded with bloatware. If you decide to root, it's also much easier on the google devices. If you know anything about ADB and command prompts, you can do it that way--and in the long run, it's the most valuable for learning about the process. If not, I've found Wugs Toolkit
to be very user friendly--although a few times I had to resort to CMD input. The greatest challenge for most users is getting the ADB/Fastboot drivers loaded. His toolkit helps with that, but I'd already had it set up before ever trying the toolkit so I can't speak to how it goes. He is very helpful when/if you have a problem.
As far as pdf annotations, there are many free apps out there (ESFile Explorer should have been free unless there is a charge for non-US markets--your use of "whilst" could indicate that). Try ezPDF reader
--the free trial version. Or, just search for pdf reader with annotations.
The best is that you found XDA. Someone is always willing to help.