I didn't get to update the docs on that. I think it's fine to tag it as 義訓/熟字訓 even if part of the term in kana. It's useful information.

@@ -9,0 +10 @@
+<re_inf>&gikun;</re_inf>

in entry 不知火/1583560 an edit with the following comment:
"since [ateji] means "contains ateji", can we interpret [gikun] as "contains gikun"?"
was accepted

in https://github.com/JMdictProject/JMdictIssues/issues/143#issuecomment-2398846443:
"we really only need to state in the documentation that the [gikun] tag only applies to all or part of the kanji in the term and not the inflecting part in kana"

while i would prefer a more advanced kanji [gikun] tag, i personally don't think it's problematic or confusing in situations like this (for example sankoku pretty much doesn't ever specify the gikun kanji) and seems to me more helpful to have than not

I don't think we're using [gikun] when it only applies to part of the kanji form.

@@ -10 +9,0 @@
-<re_inf>&gikun;</re_inf>

sankoku, daijr/s, etc.

@@ -9,0 +10 @@
+<re_inf>&gikun;</re_inf>