what you are saying may work in terms of confirming the problem, and even give you something to use to manually align. But, this will definitely hurt the workflow so I would pursue a true fix. I would definitely look closely at your rubber banding, I have seen too much pressure in the wrong place create bites that are open in spots. I have used both rubber bands and low temp hot glue for this process, I found that for all but very stable simple cases, I use glue.
Back in the day, I'm thinking 2011-2013 time frame, I had a situation where on one specific computer, no matter what was done it seemed, between the scan and design step the models would "lose" their articulation and would be off constantly. I believe it was either an issue specific to the computer or to do with the specific scanserver software version that for whatever reason didn't like that computer. 3Shape said it was our scanner and they sent us a loaner scanner, which the problem persisted on. All that said, if you eliminate all physical possibilities, don't rule out that it is simply a software error. If this is the case you will want to get a good tech support agent who can help you try solutions, such as different scanserver/scansuite versions. If you have another computer with the specs to handle 3Shape, try switching computers. It has been a long time but I have seen 3Shape scan issues that are caused by the computer, even on a computer provided by 3Shape.