Even though it is for an eSIM application, we ask for your preferred physical pickup location if you sign up with your passport as an identification document (any IDs that do not have your current official Japanese address); the whole process cannot be entirely online.
Since there are stringent laws on Voice + Data SIM/eSIM use in Japan due to past fraud and misuse cases, it is mandatory for providers to do a face-to-face ID check under the condition above.
If you have the following as an identification document, then the whole process of the eSIM application can be done entirely online:
1) Residence Card with your address registered on it
2) Japanese Driver's License
3) Japanese MyNumber Card
Please read here for further details on the procedure for receiving your eSIM: