App Proxy
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Not sure I fully understand that request. The current app proxy does already accept raw upstream IPs. How this is related to Cloudflare is not clear to me though, nor how this relates to a "private secondary domain".
You could also put the app on a secondary domain (for this an app has to support aliases though, which not all do), where that domain is not using Cloudflare. -
If you just put the IP, you are missing the host header. Cloudron itself routes traffic for http per host header internally. An app proxy currently cannot route an upstream request with a certain HostHeader to another IP than what is specified by DNS. Subsequently, you can't circumvent cloudflare, if cloudflare is active for a certain DNS entry, even when the cloudron instance might have access to a network already without routing over cloudflare.
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I think I still don't quite understand what you are trying to achieve here. The app proxy is not really for proxying to apps running on Cloudron itself, but to proxy for example apps which run on some other server and Cloudron can then provide DNS and certs as a reverse proxy.