The Personal VPN feature that allows using built-in protocols doesn’t support unencrypted protocols, presumably for security reasons:
Personal VPN only supports recommended VPN protocols; it doesn’t support legacy VPN protocols, like PPTP and L2TP.
However, that’s not the only way to implement a VPN app. You can also create a Packet Tunnel Provider to tunnel layer 3 packets yourself, or an App Proxy Provider for TCP and UDP connections. A packet tunnel provider would allow using your own L2TP implementation.
This might be solving the wrong problem, though. If this is for a specific company, why not use MDM instead of a custom app? MDM does support L2TP.