This is the process flow illustrated everwhere.
Disclaimer: The below details may be wrong. Feel free to speak up if there are any inaccuracies.
I used opensnitch to check this.
While connecting to VPN opensnitch shows outgoing connection to say 192.0.1.1. After VPN is connected the IP shown in VPN app and IP leaks website is 192.0.1.3. So the above flow would be
You > ISP > ProtonVPN server (192.0.1.1) > ProtonVPN Internal IP (192.0.1.3) > ProtonMail
So ISP can see connection to ProtonVPN server, cannot see ProtonVPN Internal IP and activities in ProtonMail. ProtonMail can see nothing more than ProtonVPN Internal IP.