Yes, I do loose the origin IP and I'm a little bugged by it. It also means that ALL traffic incoming on a specific port of that VPS can only go to exactly ONE private wireguard peer. You could avoid both of these issues by having the reverse proxy on the VPS (which is why cloudflare works the way it does), but I prefer my https endpoint to be on my own trusted hardware. That's totally my personal preference though.
I trust my VPS provider to not be interested enough in my data to setup special surveillance tooling for each and every possible software combination their customers might have. Cloudflare on the other hand only has their own software stack to monitor and all customers must adhere to it. It's by design much easier for them to do statistics or snooping.