extension.json config allows parsing relative paths via "path": true,.
Unfortunately, that functionality is limited to string values only - an array of strings (even when using "path": true,, won't get their paths transformed)
I think it's fair to expect that arrays of relative paths are also converted when using "path": true, in the config.
An existing use case it Wikibase's $wgWikibasePerRepositoryServiceWiringFiles, which is an array of paths.
Unless we're able to use an array of relative paths here in extension.json, we'd otherwise have to resort do doing it from PHP.