Your questions give me a little chuckle. I remember when I started using JRiver that I did not trust it to modify my media that I had created with a different tool. I think several months elapsed before I trusted JRiver to modify my files. That was over 3 years ago. Now I don't let anything except JRiver touch my files
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Do your due dilligence. If you are serious about media, I guarantee you will never look back from JRiver.
I am pretty sure that unchecking the one option I mentioned is all you need to do to prevent MC from changing your files without you knowing about it. You can of course initiate commands that will modify your files so be careful.
If you are really paranoid, you could share the root of your media as read-only. Then map this share to a new drive and point MC to this drive. I am pretty sure you don't need to bother with this though.
As proof, my son has a copy of my precious media on his system and he is only permitted to read (not write). I rely soley on the one option I mentioned above to prevent him from modifying my files and it has not failed me in over a year.
With regard to your iPod question, yes I believe the artwork will be transferred. As an aside, someone on this forum educated me that artwork is passed to the iPod as a magical database, not inside the mp3s.
Have fun with Media Center, and remember, right-click is your friend. I bet you will still be uncovering cool new features 2 years from now.