Point 1.3.2. regarding recruited researchers on p. 122 of the MSCA Work Programme 2023-2025 says:
“Recruited researchers can be of any nationality and must comply with the following mobility rule: they must not have resided or carried out their main activity (work, studies, etc.) in the country of the recruiting beneficiary for more than 12 months in the 36 months immediately before their recruitment date.”
If the PhD-awarding organisation just delivers the PhD (and eventually hosts the Doctoral Candidate for a secondment), the mobility rule will indeed apply to the beneficiary.
However, if it is a more complex case, for example, a Doctoral Candidate is hosted by a French lab which is based in Japan (i.e. the research organisation is registered in France, but the lab is based in Japan), then the mobility rule applies to both countries.