Well, I've done some more tests, and ... it's complicated. To reply first to John, yes, I did have an import preset active to set copyright metadata. I created a fresh scan, and then checked it in SF HDR. All was ok. I did a few random edits, and exited. SF HDR did not update the timestamp (which in itself is curious, as I understood that the "HDR RAW" option enables a type of non-destructive workflow where an edit state is added to the file. I guess it has some other way of doing this.). I then disabled the preset, and imported into Lr. Checked timestamp again, no change. SF HDR was still happy. I added a keyword in Lr - no timestamp change, as expected. Then I applied the metadata preset. This did update the timestamp, and the IPTC copyright was written to the file. Not sure this is expected behaviour. However, SF HDR was still happy with the file and recognised it as one if it's own. To cut a long story short, so long as SF HDR has opened the file once before Lr makes any changes, it doesn't care. But if Lr gets there first, SF HDR rejects it as a foreign invader....
I guess this is the very definition of "edge case", and I doubt anybody else here even remembers what "scanning" is :-). I'm not competent to judge the rights or wrongs here, but Andrew, John, I'd be interested in your opinions. I'm tending towards "Lr should not really write to a file without an explicit user instruction, but also, provided Lr simply updates standard IPTC tags, SF really shouldn't care.