Right here ember-cli-code-coverage skips calling modifyAssetLocation if the path starts with .. because it assumes it is correct by manner of being in a monorepo.
https://github.com/ember-cli-code-coverage/ember-cli-code-coverage/blob/master/packages/ember-cli-code-coverage/lib/attach-middleware.js#L107-L109

A little bold to assume it is always correct. As I understand it, modifyAssetLocation is an entirely optional configuration so the developer can override the paths if ember-cli-code-coverage doesn't get it quite right. Whether in or out of a monorepo this should be no different.
In my case (and the case of others), we need to adjust it and just end up having to do so after tests run via bash script rather than being able to just configure it here.