Please see my edit. Synonyms are supposed to be arranged by sense, so your edit actually took them further away from the correct formatting.
That's how synonyms have always been formatted as far as I know. The per-sense list would only be used if the synonyms apply to a specific sense. If this is not how it is done, then that should probably be made clear somehow.
Admittedly, common practice is a hodgepodge, and Wiktionary:Entry layout explained#Synonyms is ambiguous — even contradictory — but I think the best way to make sense of it is as follows:
- The sentence "Where several definitions of the headword exist, synonyms should be given in a separate list for each meaning" could mean that when the headword has only one sense, some completely different format should be used; however, there's no indication of what that format would be. I think the only way to make sense of this is to assume that we always use the same format, and it's a format that satisfies the above property. (The relevance of the clause "Where several definitions of the headword exist" is that the clause "synonyms should be given in a separate list for each meaning" would obviously be meaningless for cases where there only is one meaning.)
- The sentence "Use one line for each synonym, beginning each line with a bullet" flatly contradicts the previous sentences. I think it should be emended to "Use one line for each meaning". (An alternative reading is that it should be emended by adding "When only one definition of the headword exists", so that it ties back to the aforementioned sentence, but that seems unlikely to me.)
This makes it consistent with translations-sections, which are always "split" by sense, even when there's only one sense.