Having already mentioned ACES, I am going to play a little bit “devil’s advocate” here…
I am pretty sure that this thread on the ACES-forum touches the original question - namely negative intensity values due to out-of-gamut colors*. There are even some comments/suggestions in the linked thread which directly discuss insufficient blacklevel handling similar to what was already discussed here in this thread (suggesting to mis-use the “Lift” parameter of the “Raw Camera” tab to solve it).
With respect to input profiles and LUTs, I’d suggest to view this video by Daniele Siragusano, referenced in the cited ACES-thread as well, about additive mixture challenges and why they are important (skip to 07:20 if you are in a hurry). In short, you probably want to avoid non-linear operations in your input profile (that is: non-linear operations performing gamut adaptions. LUTs are usually non-linear mappings). Those things should probably come later, in the color grading step? (This video is talking about cameras looking at a real scene (light mixes linear in a scene and in the camera) - however, our scanner cameras are looking at a film positive. Which is basically a non-linear media from the start. This might require a bit of extra thinking.)
(* these negative “out-of-gamut” colors are not really a “curse” if your image processing pipeline can handle arbitray negative and positive values, like in DaVinci with it’s 32bit floating point format. But other software might clip negative values to zero and large positive values to whatever the maximum is - in the case of 8 bit data it would be 255, in the case of 12 bit data 4095 and with 16 bit data, that would be 65535.)
(EDIT: funny that we discussed some of these things nearly 6 years ago. There has been some progress I think - we all agree that all approaches will yield a basic scan from where the artistic interpretation towards the final product can start (that is, “color grading”).)