First, I am not technically sophisticated, so apologies for my likely lack of typical detail on what code's involved, etc. The origin of this report is en:Wikipedia:Help desk#Muting thanks. Currently the language at en:Help:Notifications#Muting users / mw:Help:Notifications#Muting users identically provide:
You will still receive notifications if a muted user writes or participates on your user talk page...
This exception appears to refer to ''edits'' to a user talk page. Certainly, it does not plainly indicate that even a system thanks will not be muted. Nevertheless, upon testing (in light of the linked help desk query), the notification for a system thanks from a muted user, for any edit the thanked user has made to their own talk page, is not suppressed. If this cannot be fixed/is not worth fixing, and this language was intended to capture even such system thanks, then there's no issue here. (I will go ahead and clarify the language at both help pages.) If, on the other hand, this is a bug, or can be fixed--well ... here's the report.