Disable Mail.app "special" text replacements (i.e., ... –> …) that are not present in global settings Most notably my Mail.app and Notes.app perform text replacements of .... to …, which I do not want. 

I do have text replacements globally enabled and want to keep it that way, but I have deleted a previously existing replacement rule of these ellipses a while ago and rebooted since then. Elsewhere this replacement does also no occur, e.g., while the specified replacements work fine in this input here, the ellipses replacement does – also correctly – not happen.

How can I convince Mail.app (and Notes.app) to not perform this substitution?

This is on Catalina (10.15.4).
I'm able to get the behavior you want by disabling Edit > Substitutions > Smart Dashes per app.  It appears ellipses are grouped with dashes.  

If you want to use N and M dashes, they can be typed with ⌥- and ⌥⌘- , respectively.