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This may take us down a bit of a rabbit hole but, generally speaking, it comes down to how you route traffic.
My firewall has an always-on VPN connected to Mullvad. When certain servers (that I specify) connect to the outside, I use routing rules to ensure those connections go via the VPN tunnel. Those routes are only for connectivity to outside (non-LAN) addresses.
At the same time, I host a server inside that accepts incoming Wireguard client VPN connections. Once I'm connected (with my phone) to that server, my phone appears as an internal client. So the routing rules for Mullvad don't apply - the servers are simply responding back to a LAN address.
I hope that explains it a bit better - I'm not aware of your level of networking knowledge, so I'm trying not to over-complicate just yet.
I also route everything through my pfsense firewall to mullvad VPN. I've been looking at various ways to access the internal network from the outside internet safely, and I'm a bit hesitant to open that hole just yet. Cloudflare tunnel seems like the easiest option but apparently they can see everything you put through the tunnel and I'm not real comfortable with that.
Does one need a dynamic dns to use wireguard to tunnel back in, or is there another way of ensuring you can connect to the correct location? Does the wireguard server run on docker?
You do need to be able to reach your public IP to be able to VPN back in. I have a static IP, so no real concerns there. But, even if I didn't, I have a Python script that updates a Route53 DNS record for me in my own domain - a self-hosted dynamic DNS really.
You certainly can run Wireguard server in a docker container - the good folks over at Linuxserver have just the repo for you.
Thanks, I'll give this a shot in the coming week!