I've tried all the non-armored boots in Skyrim and Dragonborn DLC and none of them look good with the Archmage Robes - they clip horribly.
I hope Beth can delete the enchantment on the unique boots in the Archmage's quarters so we can add our own.

Or they can make unenchanted versions those boots available in the future DLCs.

Edit: hmm, I was in a different forum than I thought I was in! sorry!

Unique boots in the Arch-Mages quarters? You mean the item 'boots' with the shock resistance enchantment? I'm fairly sure they're just generic boots - the same as the ones given to you by Mirabelle Ervine when you first join the College.

Unfortunately, they're not the same. The unique boots with shock resistance enhancement cannot be found anywhere else (I wish they are unenchanted). They have a unique appearance and the only pair of non-armored boots that visually works well with the archmage's robe.

Oh, really? All this time and I never knew!
Well, if there aren't any boots without clipping issues, I'd say Bethesda definitely ought to fix that.