You are clearly approaching this in a careful and deliberate way (good). Hands on experience will help you make up your mind: there is nothing like holding one of these cameras, and using it, going through the sometimes complex sequence and seeing how you like it, or don't. No Internet research can replace that. In the end, its still tactile.
On the issue of shimming and alignment, there are two different strands to consider:
1) the actual alignment and focus of the camera to the back
2) your source of information and control over that.
The two are only somewhat related, much different than on a DSLR. For example, the alignment of the back to the lens plane is critical. They can get knocked out, that's why the change in camera profiles in the past 10 years: wooden field cameras were too flimsy, Hassy went to a closed system to have precise control over all the pieces, why Leica gave up the DMR and went to the S2 (internal control over the sensor and its alignment). Everyone recognizes the need to control of that alignment. Once its set, its usually stays in place. Setting it is typically by shimming. How to check? Tethering, live view, check the 100% focus, etc.
Part two of this is when you take your picture and exercise your control, that is, you focus, and believe it to be in focus. This is a very different matter, as what you think may be in focus may not. Some sort of calibration between what is real focus (per the camera) and what you think is in focus (what you see) is needed - the best way is live view, checking 100% on the screen or tethered computer. There are other ways, such as using a distance measurement and then adjusting the lens per helical settings (a la Arca) . Lupe on GG is another (remember, the GG has to be in exactly the same plane as where the back is....). The validity of each these has to be checked against the reality of the lens:back setup.
Some MF cameras, such as the SLR Hy6, incorporate these adjustments by allowing for "focus adjustments" for each lens: first you calibrate the lens:camera:back (checking by tethering and live view) to achieve maximum sharpness. Then note your settings for each lens. When that lens is mounted, you dial in that adjustment on the camera. Pretty neat, yes? This is combining adjustment for each lens, its mounting (the first part of the puzzle), as well as incorporating any necessary adjustment of focus screen (or focus confirmation) to the back (second part of the puzzle). Sounds complicated, but is really not.
In short, both parts have to be confirmed: First get the lens:back right. Then calibrate your control so when you think you are in focus, you really are.