What's the difference between [connecting to a TOR channel from a server provided by the VPN and then navigate with your favorite browser] and [connecting to any server with Proton and THEN opening and navigating with TOR browser?]

What I love about Proton is the ability to keep custom profiles with different servers and protocols

The difference is that Proton’s Tor servers will route your entire connection via Tor, and connecting to regular VPN server and then letting Tor browser connect on top of that (Tor over VPN) will only route your Tor browser through Tor. Both conceal from your ISP (or anyone else) that you use Tor and also from whoever runs the Tor entry node your real IP address (if it’s not leaking).

With Proton Tor servers you can connect to .onion sites via any browser but this is highly not recommended. Tor browser (unchanged) and Tor network need to work together to provide anonymity (you should also not log in or use identifiable information while on it). If you use any other browser you are extremely identifiable (via browser fingerprinting) to the point that it’s even worse than regular fingerprinting (since only a tiny barely registering amount of people surf Tor compared to the regular internet) and you’ll miss Tor browser fingerprinting methods which also rely on “hiding in the crowd” (everyone using the same settings).

Just use Tor via Tor browser (over VPN). Also you need to read about Tor before you use it.

If that’s the case, why is Proton offering a service that cn be dangerous for you? Should I just ignore the possibility to Tor over VPN via the VPN without touching the Tor browser and instead, connect to the VPN and then switch to Tor browser with the default options whenever I need to access onion sites?

While I really like the Proton suite, I feel they over-hype and over-market. Take the climate activist kid who got busted when Proton gave up his real email IP. Proton advertised on their main web page they did not log IPs. When I signed up for Proton a couple of years ago I knew this was tricky wording as they may not log your IP, given the way SMTP PGP email works they can’t prevent themselves from accessing you IP. Thus I knew to use an always on VPN with kill switch for Proton Mail, but those not tech savvy would be fooled by that statement. You also have to realize Swiss law provides Swiss authorities can demand your Proton Mail real IP (thus mask it with a VPN), but Proton does not have to (and does not) reveal your real IP with Proton VPN under Swiss law.

Without them saying it, I think the point of the Proton Tor/onion website (not the VPN Tor connection) is that in that case Proton can’t see your real IP. Download Tor and use it to go to the Proton Mail Tor/onion website and Proton can’t see your real IP. A safe way to sign-up for Proton services without revealing your real IP, and then use Proton VPN to mask your real IP from Proton Mail as Tor is slow. Still have to pay with a crypto or cash to maintain your anonymity from Proton. And to further this, Proton needs to accept Monero as the truly anonymous crypto if they already have not done so.

As for Proton VPN connecting to Tor (as opposed to you using the Tor browser with PVPN already on) I see it as a marketing gimmick. Brave browser does the same thing. Without getting technical, it’s not that the encryption is insecure per se, but rather since you are not using the Tor browser, you can be fingerprinted for ads or by adversaries. I’m not a fan of Proton doing this, but overall I like their services. Problem is with the two examples I gave, Proton has put people who are not tech savvy in potential and actual compromising positions.

And, ideally, you should use Tor separate from a VPN in most use cases.

It’s not “dangerous” if you know what you are doing. There are secure operating systems that route your connection through Tor. You might want to browse .onion sites and Tor services outside of Tor browser and understand what you are doing. You might prefer Tor’s 3 hops which from a network perspective are much more secure (technically) for everything on some machine. By offering that Proton also connect you to Tor via VPN anyway. It’s just another feature.

That’s also my problem with Proton. I ultimately don’t trust them, but I like their VPN service and app better than every other. Security wise, I think your best bet is mullvad, but it offers less interesting features and the app is a bit harder to use.

My point was Proton stated thy did not log IPs on their main website and have changed that after backfire from logging the IP of the French activist and handing it to Swiss authorities.