X-arcade USED to sell the encoder board separate for about $60, but last I heard (4-5 months ago), they weren't anymore.
They have an 800 number - 1-866-942-6464
M-F 9-5 Eastern, which might get you faster answers.
In a worst case, it's likely the X-arcade solo uses the same encoder as the standard one, so only $100 instead of $150 (Ask first, though).
Beyond what you mentioned, I'm pretty sure the X-arcade is positive ground, for lack of a better term. In other words, while virtually all other encoders supply +5V on the input terminal, through the microswitch and back to a common gnd; X-arcade supplies a common +5V to all microswithches, through the switch, to an individual GND at the input terminal. Works the same in practice, but you will not be able to hook up Perfect 360 joysticks to it, if that would be a concern.
No shifted inputs, AFAIK.
Reprogramming - yes and no - it's stores four codesets, (3 user-selectable) selected by a rotary or slide switch and programmed as shown here
http://www.x-arcade.com/htm/programming.shtml. Note that there is no software for programing, no way to load different codesets from software, and no way to keep more than 4 codesets.
I thought the connector was 9-pin serial, but don't have one, so don't know.
If so, you might be able to get a serial switchbox and use it to switch between the different adapters.
If not, it could still be done, maybe with a switchbox and either adapters or modifying the cables so they're compatible with the switchbox, but I don't know if it would be worth it.
Best solution is probably to hack a PSX gamepad and then use -
PSX-USB adapter for MAME
PSX-X-box adapter for X-box
PSX for PSX
etc.
Might be a way to hook this up with a switch to select. Search the threads, others have done this.
Next best solution is probably to use a commercial encoder (I-Pac, KeyWiz, MK64) and a hacked console gamepad, with some switch to select between the two. That's been discussed before as well.