Deprecated message groups
That would be great. iNaturalist mostly occurs in sets of translations with the same content.
If by "sets of translations with the same content" you mean translation memory suggestions, which appear in the sidebar, then yes, they are kept, and this is more or less the intention. (Nike can correct me if I'm wrong.)
If you think that it's a problem, it can be discussed. I think that it's mostly useful. Occasionally, I even edit iNaturalist translations into Hebrew if they look wrong to me even though they probably won't be used by iNaturalist, because I want the translation memory to be correct and useful.
I mean Template:Identical (e.g. ). Translation memory is only given in selected languages (Special:Preferences#mw-prefsection-editing) and depends on the message group. I agree iNaturalist messages should be kept and may be useful for further reference so I also translate them. On the other hand, I'm glad to note iNaturalist is not included in Special:LanguageStats anymore as I have already translated it once (on Crowdin). As to Wikidocumentaries, I would be glad to translate the messages but as far as the status remains unclear, I'm leaving this for later when more active projects get translated.