There is a rare occasion where "dirty" references are actually needed - BTB's Game Improvements even has a handful in the "Equipment" plugin. OBviously, the vast majority of the ones in GDR are not amongst those rare exceptions. Darknut's concern - to which I am largely sympathetic - is that people would just run the plugin through TESTool to "clean" it, which would indeed break it.
Well, i did not find any dirty references in the "Equipment" plugin. There are a few of the typical "AMBI" entries when editing a cell, wich can be safely removed. And there is no way that the removal of these few entries would brake your mod.
As regarding Darknuts GDR, there have been reasonable posts in the past stating that cleaning with TES-Tool will not break the Mod, which i can confirm. These people played through the mod, so did I. I checked every deleted entry in TESTools-Log and found nothing removed what would be needed in order to function.
I guess that there i a misunderstanding in defining what a bad, or dirty, Reference or entrie is. The actual references in your mod (not the AMBI), for example, are nessassary in order to function (e.g., the repaired daggers). There are not dirty and will not be cleaned away by TESTool. As no deliberate changed GMSTs (i recently read in a post that TESTool would do that) will be touched. I am sympathetic to Darknut as well that, in order to all the myths an d misunderstanding, he might feared that TESTool would clean away essential functions.
The problem is just that nobody has wanted to be the one to go through, determine which "dirty" references truly do not belong, and deal with them as they should.
I would say it is the other way around:
The problem is just that nobody has wanted to be the one to go through, determine (and actually proove) which "dirty" references truly will break the mod. - If asked, the only answer one gets is "it surely will break this mod", but never what actually would break the mod