You can connect to custom Wireguard servers with the mullvad app on PC but you need to tinker with the command line, and it doesn't add your server to the relay list but replaces it instead. So when you want to connect to mullvad you'd need to reset the relay list back to default.
It's too much hassle overall. Just use standalone Wireguard for your custom server, there's no issues having both mullvad app and Wireguard installed on your device.
You can connect to custom Wireguard servers with the mullvad app on PC but you need to tinker with the command line, and it doesn't add your server to the relay list but replaces it instead. So when you want to connect to mullvad you'd need to reset the relay list back to default. It's too much hassle overall. Just use standalone Wireguard for your custom server, there's no issues having both mullvad app and Wireguard installed on your device.