As I checked foreign (mainly Europian) method, the coastlines are included in administrative boundary relation.
My correction is here.
relation/4538785
osm.org/#map=18/34.25797/136.58167
Is this method similar to your intention?
If yes, I'll apply it to the other municipalities as clean up.

I'm now working on next (Aichi prefecture) import.
I'll care them after Aichi import action.

Thank you for your feedback. It needs clean up indeed.
Please let me clarify the policy to fix them.
I guess we have 3 approaches.
Which one is your thinking of?
If they all wrong, could you tell me the sample relation id as our ideal one?

1-1. delete island_admin boundary ways.
1-2. redraw them as same as geom on coastline.
1-3. set new admin boundary way to relation as outer role member.

2-1. delete island_admin boundary ways.
2-2. add boundary=administrative tag to coastline ways.
2-3. set them to relation as outer role member.

3-1. delete island_admin boundary ways.
3-2. delete coastline_admin boundary ways.
3-3. enclose admin boundary ways using the way on sea.
Result should be like this.
relation/4089279

But I guess 3rd is not landarea boundary, it is similar to maritime baseline.

Thank you very much!