No problem with exFAT! More than that, is the only option to manage files over 4 GB if you use options for that... Just, you can't do the firmware upgrade (and so, the first ML install in your camera) from an exFAT-formatted card, must be FAT (and so, 32 GB or smaller), if not camera will not find the firmware upgrade. After that, you can use exFAT cards without problem (I always use exFAT with no problem att all).
When I told before EOSutility, I meant EOScard you'll find in
http://www.magiclantern.fm/install.html, my fault....
Re-read install procedure, and go through it carefully, as you've been told.
I'll remember you all you have to do, but, even so, please, read instructions
http://www.magiclantern.fm/install.html again to double check. I'm talking from memory...
1. Format your first card, low level in camera, and choose to eliminate ML (if you've not doing so yet) to return stock your camera (really, just to erase ML files from card, an erase the booting from sd flag from camera.
(1a. If you want to be even more sure, download and copy on card the original 600D 1.0.2 firmware from
http://www.magiclantern.fm/install.html, and do firmware update on your camera. But not needed at all)
2. Format low level in camera your other cards intended to use with ML. (If you want any of them in exFAT, for sure for an 64 GB card, but can be alsosmaller, you'll have to do formatting in computer, usual way, choosing exFAT)
3.- Copy the files from the official stable 2.3 ML release into a FAT formatted card, specially including the EOS 600D firmware update file. If you want to use a more recent beta build (as I do), then, download it and overwrite the corresponding file/folders in you SD.
4.- Insert card, choose M mode, do restore default settings on your camera, and do firmware upgrade from Canon menu. You've yet enabled boot from sd in your camera, and this card is done bootable, so, you can use ML with it.
5.- For other cards:
5a.- If they are in FAT (and 32 GB as maximum) you can just go through 3. an 4. again. Cards will be ready when firmware upgraded (even if it was yet upgraded)
5b.- For any card (but compulsory for exFAT ones, or SDXC ones). Download EOScard (or the options for other OS... but the linux one didn't worked for me) from link in
http://www.magiclantern.fm/install.html, and mark, as shown there, the card as bootable (check image there), and save changes. Copy ML files (autoexec.bin and ML folder) into the card (if using a new beta release, I'm nor sure if they are complete... I alwas copy at first files from the official 2.3, and then overwrite with the beta ones). Should be working.
All clearly stated in
http://www.magiclantern.fm/install.html