Rick, I can also ask Gerry, George's guitar tech or George that question in the dojo and if they don't mind, I'll post what they say here.
Craig's post of what Doug said is right, I was told that they were looking at the merc transformer but George liked the stock RM100 transformer at higher volumes. And of course there's the tubes and cosmetics as mentioned before...
I have both the Lynch box and the rack setup--the RM4 and the RT250 poweramp. I have not had all of the rack stuff in the rack since having the Lynchbox--the poweramp is sitting by itself in storage at the moment so I can't say anything in regards to doing any type of A/B comparison. Right now, I have just the Rm4 and a lexicon mx200 (I love the lexicon delay through the fx loop!) I've been running the RM4 through the LB power section for recording purposes. Anyway, what's great about the rack set up is that with the RM4, of course you have 4 modules instead of just three--but you can also have a lexicon mx200 like I have in there all wired up and ready to go ( and they are very reasonably priced) and as for the poweramp, it has two channels and you can run them together or just one at a time. One channel is EL34 powered and the other is 6L6 powered. I have a Genz Benz G flex 2 x 12 cab and it has both single and stereo inputs. I can connect to just the mono jack and run both channels through both speakers or I can choose either amp channel. I can also connect one side of the poweramp to one speaker and the other channel of the poweramp to other speaker via the stereo jacks and run stereo--with a slightly different tonal mix from the two different tube power sections. Lets say I want to play some blues, I can switch to just one 12 speaker in my cab with the 6L6 powersection and use a deluxe or tweed module and get that Fendery blues tone... I can also switch to the EL34 side when I want a Marshally tone--say with a Brown module or SL+. Or I can run in stereo--6L6 and EL34 at the same time--separate speakers. There are lots of tone combinations and cab configuration options with the rack set up. the rack set up--to me, is hands down the most convenient and most versatile setup. But I sure do dig the mojo of the Lynch box--the look of it and it is no doubt an elite amp.
I don't like to lug around 4 x 12's so I'm using the Genz Benz G Flex 2 x 12. I found out that I can get the Randall 2 x 12 covered in the Lynch color scheme at a reasonable price--really about the same price--green with gold piping and gold logos/Lynch logos... but it's not ported so I don't know how it would compare to the Genz cab which is the best closed back 2 x 12 out there IMO . I mentioned to the Randall rep I know that they ought to do a ported 2 x 12 and he pasted that info along. I got the idea that If enough people ask about it, I would not be surprised to see that happen. Randall seems pretty receptive to input from customers.