As investigated in T251898: Validate TwoColConflict interface on Lua and JavaScript pages.
As described in T251898 the suggestion is to disable TwoColConflict on all pages where the content model (should be preferred over content format) is not CONTENT_MODEL_WIKITEXT or CONTENT_MODEL_TEXT. This should have the same effect as excluding pages by file name extension or namespace.
There are some .json pages on Commons, e.g. https://commons.wikimedia.org/wiki/Data:I18n/EditAt.tab. Since JSON is effectively a subset of JavaScript, the two should behave the same.