The modules listed on Randall's web site are stock modules.
When people talk about modded modules they are talking about changing/adding stuff to the circuit board of a stock module to get a different sound.
Check out http://www.jadedfaithmods.com/ and http://salvationmods.com/
There are also some smaller modders and folks here that mod their own stuff and can help you out if you are handy with a soldering iron in the DIY forum.
The stock modules sound great. The modded modules are just fantastic. For the price of a boutique pedal you can get a [insert $5000-$30000 amp name here].
As far as differences between the actual amps, other than which tubes they ship with I'm not sure there is much difference at all.