score:2
I found the answer myself. The below PDFs dated 2021/11/29 state that re-entry permission is still valid.
https://www.moj.go.jp/isa/content/001347330.pdf
次の(1)から(4)のいずれかに該当する場合には,特段の事情があるものと
して上陸を許可します。
...
(1)再入国許可(みなし再入国許可を含む。以下同じ。)をもって再入国する外国
人
https://www.moj.go.jp/isa/content/001359621.pdf
If any of the following (1) to (4) applies to the foreign national, landing
will be permitted on the premise that there are special exceptional
circumstances.
...
(1) Foreign nationals entering Japan with re-entry permit (including a
special re-entry permit; the same applies hereinafter).
Permanent residency carries with it re-entry permission, and so permanent residents are allowed to re-enter Japan even under the current restrictions.