I have seen hundreds of "custom sets" assembled in 2 stores. I've seen cars swapped in or out by request, or damage necessity. From a point of sale view, there is no way any book could cover this. But I still consider it a set. Just not a "factory set".
Many in store buyers would demand a sealed box be inspected. It was a consumer that had the power back then Lots of boxes with one extra tape strip right. Sears here even had some Lionel tape, and a Lionel supplied repairman sometimes.
So a point of sale variation can exist, but without dated, listed items, or photo of say that Christmas or birthday, or a run on a layout soon after, its just a nice "custom set" to me, not a point of sale variation. No proof of originality for me, no extra bucks for you.
Factory sets and their variations are the "confirmed" collectibles in my eyes. But its next to impossible to confirm 100% the originality of sets unless never opened. So listed cars being replaced with a duplicate, not a big deal.
I think set variations also occurred at the factories unrecorded.
It all comes down to the personal documentation in hand on those to.
I.E. I take it all with salt. Is it worth it toMe!