Not my expertise I’m afraid. Geoip blocking is straightforward with traefik (and Pangolin docs), Crowdsec is a little more complicated, and with the external firewall into the VPS, there isn’t much more I can think to do.
It’s likely more a factor of how secure Pangolin itself is at that stage.
If today’s outage is anything to go by, you’re better off not using Cloudflare!!
I have continued to use it for public websites so that, in my thinking, at least the Cloudflare network is scrutinising who is accessing my webpages in case of attacks etc.
Pangolin is a simpler cloud reverse proxy, whereas Cloudflare has more bells 'n whistles for quick-set security. You just need to harden your VPS that Pangolin runs on. You can activate Crowdsec etc on it as well.
I run mine on a Hetzner VPS which has a nice firewall feature in the control panel securing the VPS ports for SSH and Pangolin tunnel to my home IP. Then it’s only ports 80 & 443 exposed. And I think from memory Pangolin doesn’t play nicely with UFW (well, Traefik doesn’t).
I only started using Cloudflare tunnels recently, but I’m now using the self hosted alternative Pangolin on a VPS for private services, and I keep the Cloudflare tunnel for public web hosting, i.e WordPress. This also allows easy restriction to the WordPress login page for other users via Google auth etc which is something very simple with CF.
Having split up my private/public services to seperate tunnels also means I don’t stand the chance of taking the public services offline with my constant tinkering of Pangolin and the VPS it runs on.
I have pushed the CF tunnel for file transfers occasionally (which is against their terms), but it hits remarkable speeds for a ‘free’ service.
Pangolin is a reverse proxy, so it can forward a URL to any backend service on any port. But you’re right in that you have to be signed in on the browser you access it on. Therefore an app won’t directly work without prior login. You can create a ‘shareable link’ in Pangolin, which I use for the Immich app. This gives me header tokens that the Immich app can take in its advanced settings, and that’s how that one works.
I’ve recently moved away from dedicated apps for mobile services and toward web-based access for most things (I use Music Assistant in browser). This isn’t perfect for everything and everyone, but I realise now with your question that it’s worked well for me transitioning to Pangolin (and at least Immich app works).