64 bits memory doesn't do very much in this case.
in this case, this is not specially doom. and this is not specially graphic card too.
this is simply the effect of the 060 wasting ton of clock cycles to read/write in memory when the bus is divided by 2... it's not very hard to understand.
it's a bit like if you get a car engine from 72 to 100 HP, but divided the gas pedal run by half. (i don't know if "run" is the good word in this context but english is not my native language)
look : here is my Mk2 at 66 Mhz 1:1 bus : https://www.youtube.com/watch?v=nPKMsKGj_1g
compare here at 100 Mhz : https://youtu.be/9zCHGWytf9Q?t=73
what do you see ? and please watch carefully 
i have a very little bit better framerate at 66 Mhz... why ?
because at 66 Mhz, the bus is synchronous, and the 060 despite the fact there's less raw mips... waste a lot less clock cycles to access memory.
The first sentence you wrote in that post made me ignore everything else you have said.
If a 64bit memory access would not matter "that much" your MKII would recive the same FPS as your MKIII did, sure you had a 9Mhz differnce but that would not drop you from a stabel 25-30 fps on the MKIII to a 16-19fps on the MKII
And then we take a look at the video where MKII 66mhz vs MKII 100Mhz
Here we can see maby 1-2 fps difference in some areas at most, its very hard to tell them a part.
So if you where running a application that where not that memory hungry like Doom and would use the CPU more the 100mhz MKII would win by a long shot.
Run a timedemo and you will have a easier way to see the FPS difference.
