This is going to be philosophical rather than methodological,,,,but my comments are at the heart of your basic question, which I believe is, "Where should I set control limits?" If one goes back to the fundamental purpose of control limits, they are limits which provide a signal for economically balancing the risk of making two mistakes:
1. Searching for assignable cause variation when in fact none is present.
2. Not searching for assignable cause variation when in fact it is present.
The key phrase above is '...economically balancing...'. There is nothing magical about any mathematical algorithm to calculate control limits using good old fashioned Shewhart derived limits or otherwise. Shewhart himself said his process seemed to 'work' practically in a wide variety of settings. So if you can justify 'where' you set your limits from an economic balance point of view...then nobody can tell you your limits are inappropriate. From your narrative it sounds like you are thinking along those lines...but only you and your process knowledge can appropriately apply this economic balance thinking.