No clue of exact details, but I always thought it was a feature level thing, E for economy L for Luxe or something. So maybe more onboard on the L ???

Both E and L revisions have RAID option. AFAIK, difference between CUBX/CUBX-E/CUBX-L is superficial. Original CUBX has UDMA66 RAID, but UDMA100 won't help you much on a 440BX, due to bus limitations.

UDMA 100 doesn't help you much with anything, until about 2005 when there were some spindle drives starting to break 50MB/sec in the MIDDLE of the drive (Hitting 70 on the first couple of tracks is niiiiice, but what about the rest of your apps?) But yeah, after that, just before it's all SATA, there's briefly a point to UDMA 100 and 133, especially with RAID.

CUBX - additional IDE controller and VIO regulator (3.5/3.6V for PCI/AGP/chipset/RAM)
CUBX-E is an additional IDE controller(different then at CUBX), but without a VIO regulator.
CUBX-L is the same board as CUBX-E, but without the additional IDE. Well, without the Vio regulator.

At the moment, the external IDE controller does not matter, and to install the old OS you need a floppy disk with a driver.
Thus, either full CUBX or no difference CUBX-E/L
Vio regulator can be both useful and harmful. For example, with a powerful video card.

You don't need a driver to install OS on this controller. Utilizing onboard controller BIOS and INT 13h it works even under DOS. In fact you will get a performance boost, because it somehow applies UDMA transfer mode. Note the linear read speed:

This is on CUBX-E with integrated Promise Ultra100 controller. You will not get this speed using onboard IDE controller, because then it will use PIO mode.