I believe you are correct. From the Tools->Options->Tags->Mpeg screen, the ID3v2 “write” formats are radio buttons – only one can be chosen. It will write ID3v1 and/or APEv2 and/or ID3v2 tags, but only one version of ID3v2.
So, to insure you have only ID3v2.3 ISO tags in your files you should:
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Select ID3v2.3 ISO tags as the kind to save
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Select all your files and choose “save”
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Specify ID3v1 and APE tags as the kinds to remove
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Select all your files and choose “remove tag”
Write ID3v2.3 tags before removing anything just in case some of your files only have ID3v1 or APE info. Once you know your tag info is safely recorded in ID3v2.3 format, you can remove any ID3v1 and APE tags.
Don’t forget the ExtendedTags and CustomizeColumns steps above. I found some unexpected junk doing them.