You think the 1x16 types may concentrate on Passenger while 1293s will replace them on Freight services? They also have tests on 1293s with passenger trains...
They do have tests, but as it stands now, 1216 are indeed being replaced by 1293 on freight; not everywhere but in a sufficient amount that more are available for passengers services.
So they've given up on 1116201 being on set 01, 1116225 on set 25 etc as some locos are restricted, for example 1116201-223 are the only Swiss equipped locos.
To answer your question: I had a look in the appropriate spotters‘ forum and it seems to me that while they apparently try to keep locos and sets together (probably, as you said, to make it slightly easier to diagram them) it is really hit and miss and you can find lots of different combinations.
Doesn’t change the fact you pointed out that diagramming RJ sets is very complicated due to the different limitations on which sets and locos can run where.
In the case of a (unrealistic) Innsbruck - Lienz service, as I believe the hardest part would be to diagram the set, since only sets 52-60 are able to run in Italy; finding a 1216 should be easier in comparison. And in any case, the number of RJ sets is always an issue... they are diagrammed quite intensively and are scarce.