Yes, tuning with 9v would be better than 12v. It’s just about the worse thing you can do to an MTR adjusting a connected tuner. Steve Weber designed a tuner to compliment the ATS (MTR) series of rigs which incorporates a switched load, that way your rig never sees a really bad SWR. OK1CDJ sells a nice kit which is very closely based on the KD1JV design.
All the MTR series rigs are very close in performance, there’s a few tweaks here and there, but there’s not much difference between them. The first two versions were two band, the first one was board only, the second version included a steel and aluminum enclosure made by TenTec. There were very minor circuit changes between the first and second edition 2Bs, nothing of any significance. The 3B was first offered as a self build kit, again with a case by TenTec, but this time all aluminium. The 3B weighed around 120g versus the 170g of the 2B which came before.
LNR Precision started making the MTR-3B available as a fully built, or mostly fully built, rig, whereas the 2Bs were only ever available as self build kits from KD1JV.
The MTR-3B is pretty much just a 2B with firmware change and an extra set of filters (RX and TX).
The MTR-5B introduced the nice LCD display and also internal switched mode voltage regulation, this reduced the RX current quite a lot. Later LNR Precision MTR-5B have a different display with less lines but apparently it’s much easier to read. The RX and TX performance is pretty much the same as the other MTR versions.
The 4B is a re-worked MTR-5B which uses a set of 4way slide switches instead of the two banks of 3way switches in the 5B, this makes for simplified band switching.
My MTRs are all built from the KD1JV kits, I’ve not had much experience with the LNR produced units.