Can you (Mage's Guild question) (Spoilers)

[Ragin Cajun]

When you assume control of the Mage's Guild...are there any major perks beyond the magic root chest (which does not work on Ninroot I've noticed)? Can you ever rebuild the Bruma Guild?

[Moot]

Apologies for bumping a slightly old thread, but as nobody has answered your question I felt the need.
Quoted information was taken from [url="http://uesp.net/wiki/Oblivion:Confront_the_King"]this[/url] page:

Now, as Arch-Mage, you have a few benefits that go with your position. This includes the Arch-Mage's quarters in the Mage's Tower. The quarters include its own spell making and enchanting apparatus.

After speaking with Raminus Polus about an ingredient collection, he will direct you to Julienne Fanis in the Lustratorium, whom you should also ask about an ingredient collection. She'll explain the use of the Enchanted Chest in the Arch-Mage's quarters. Once a week you can place one ingredient in the chest and within 24 hours it will turn into a larger number of the same ingredient. (Note: After a week, the Chest will be cleaned out.) Some special (and a few not-so-special) ingredients will not work.

Also as Arch-Mage, you can ask any of the Mage Apprentices at the Arcane University to follow you. Talk with any of them and they will ask you if they can help. You can ask them to follow you, wait, and go back to their lesson. There will be up to 5 Apprentices willing to follow you; in some versions, only one Apprentice will follow you. If you ask another, he will state that he's "busy right now".

Caution: The drawers at the end of the Arch-Mage's bed resets itself periodically, so storing items here is not advised. The nightstand next to the bed does not respawn but still has scripts on it so again it is not sensible to store items in it.

If you have already completed the Thieves Guild quest Misdirection, Hrormir's Icestaff will be sitting at the foot of the bed when you enter the Arch-Mage's Quarters; picking it up at this point is not a crime. You can also find the note from the Gray Fox in the night stand. Activating the nightstand again will remove the note from your inventory.

I'd also like to point out that if you are on the Thieves Guild quest Misdirection while you are the Arch-Mage, taking the staff is not considered a crime. Also, when the staff is returned, it is conveniently recharged (for free, at that).