Fork length really does affect the ride. I cannot stress that enough. Get it wrong, and you will destroy the ride.
I commute on a lovely old steel Avanti Hammer MTB (also v large, circa 1998), originally designed for a 63mm fork.
Currently it's got a 100mm travel Duke XC in it. Commuting is okay - very, very stable at speed, but lacks responsiveness when weaving through the traffic (I am an ex courier/messenger - so I like to get ahead when the traffic is stopped/slow).
What cheesed me off was, after a few months enjoying the "feel of steel", I chucked some knobbies on her, to go out for a thrash off road*. What a dissappointment!
Singletrack was a chore! The sweet 71 degree head angle had porked out to about 68 degrees. Slow to turn into corners, the bike's front end felt floppy out of the saddle (known as "wheel flop"), and the front tyre would push out in hard turns (understeer in moto speak). I didn't want to ride it offroad again.
So, as you have identified, don't do it! I have sourced an old Marzocchi Z2 Superfly (70mm) to chuck on it, and expect big things (singletrack bliss) in the future. 100m is overkill for my road commute anyway.
I have owned Marzocchis, Rockshox, Lefty's, Headshox, Scott's, and RSTs over the years, and they all have positives and negatives.
Both the Marzocchis you have mentioned are great forks (reliable, with quality travel).
If you spend most of your time with both wheels on the dirt, for for the MX Comp. Good weight, great seals, and will deal with all but huge drops/jumps.
Pricewise (at least here in Australia), they represent excellent value as well.
* I have far too many bikes, but every new one I build up is like a new lover - some are good, some are not so good, but occasionally one comes along that makes you redefine your past experiences