FYI, I created an issue on the LOOT GitHub page regarding the ITM that Kinaga mentioned shouldn't be cleaned. I let Kinaga know on the Nexus page, and I was surprised by this response:
Since writing that I have noticed that removing the record may not actually prevent dialogue from functioning. It just seems to be a record that is automatically generated by the creation kit but AFAIK not actually used by the game. This means that it probably shouldn't fall under the same "dirty mod" category as other ITMs since it cannot possibly cause any problems, but at the same time it may not be necessary so might be better left out in the interest of efficiency.
Sorry about the outdated info. The record itself relates to steward dialogue, which I actually did edit, and so I thought that TES5Edit was simply unable to recognise my edit.
The issue here is whether ITMs in DialogueViews should be considered to make a mod "dirty", since I don't think the game engine reads DialogueViews at all. At the time I wrote the quoted line I suspected that I had edited the DialogueView in a way that TES5Edit did not recognise, however I now think that the DialogueView is used only by the creation kit itself.
I intend to remove this edit from the mod in its next update. It might be a good idea to set up a rule for LOOT to ignore ITMs in DialogueViews since they are not used by the game anyway so cannot cause problems (assuming this information is correct).
It looks like cleaning it may not cause an issue, but leaving it shouldn't cause an issue, either. However, I am not familiar enough with the technical bits to really know. :-/
I assume leaving the ITM for now shouldn't hurt anything.