macOS app review process: Touch Bar functionality in metadata
At this stage, I'd advise you to submit a technical support incident. As a paid member of the Apple Developer Program, you are eligible for 2 technical support incidents in a year. It involves getting access to an engineer from Apple's development team and basically get code level assistance.
- Requesting Technical Support
A Technical Support Incident (TSI) is a request for code-level support for Apple frameworks, APIs, and tools, and is available to members of the Apple Developer Program, Apple Developer Enterprise Program, and MFi Program. Submit a TSI if you cannot fix a bug, have trouble implementing a specific technology, or have other questions about your code. Your incident will be assigned to a Developer Technical Support engineer who can help troubleshoot your code or investigate possible workarounds to fast-track your development. Support is provided in English via email, typically within three business days.
You can have an engineer look through the issue and advise you in what may be possibly causing trouble getting your app approved.