I just bought the ONDU multi-format 6x12-6x9-6x6 pinhole and so far exposed and processed one film, Fuji Acros 100.
I've found there is a particularity to using the 6x12 format, because of the spacing, the use of the 6x6 window and the spacer bars for the 6x6 format.
When the first frame number, 1, is in the red window, it would be fine for 6x6 because there would be leader film to the left of it, towards the take-up spool. The 6x12, however, with frame 1 in the window, is not sufficiently advanced. As a result, the first frame was cut off and the image size is about 10.9cm, with no clear film leader. When I cut the film from the backing paper, it was at about 1cm from the edge of the tape. Had it been cut right to the tape, that still would have been a problem, as there still wouldn't have been any clear film leader. Pulling the tape off isn't an option, either.
At the other end of the film, after the last frame, there was a good 7cm of blank film, so there is plenty of lee-way to compensate by winding past the number seen in the window - if, that is, the number CAN be seen in the window. As the OP said, it can be difficult if not impossible to see the number on the backing paper, but I find the frame numbers on the Fuji Acros are clearer than on other papers such as Ilford.
About 2.5cm past the frame number, the first of three small circles will appear. They are the lead-up tp the next frame number. By my calculations, advancing past frame 1 to the second of the small circles will then place the film correctly in order to have enough film and leader for the first exposure.
My plan is to then advance the film until frame 3 is in the window, and then again to the second of the small circles past frame 3, if I plan to continue taking photos in that particular session. If I'm not going to take any more photos, I'll leave the frame at 3, with a reminder to myself to advance the film again before using the next time.
Alternatively, the film could be advanced to the second circle past the frame number, since if there is a doubt as to how many frames are exposed, the film can be wound back slightly to see what frame it is, then advanced again. Being careful and taking good notes for each frame and film is also helpful, but there is no guarantee that always happens - speaking strictly for myself here!
Also, since these cameras are hand crafted, the spacer bars are not interchangeable from left to right, so I've marked which side each belongs on, and facing which way.
So far, so good, I'm pleased with the results of the first film and the quality of the camera and pinhole. Here are a few from this roll, starting with the first frame which was short changed.