I have two virtual networks that each have their own virtual network gateway (VNET1 and VNET2). I have connected them with VNET to VNET connections. All resources in each VNET can see each other via PING as well as RDP so I know the VNET to VNET connection is working properly.
I also have a Point to Site configuration setup on VNET1 which allows me to VPN from my onsite premise. When I start up the VPN connection, I can see everything in VNET1, but I cannot see anything in the other VNET (VNET2).
Shouldn't I be able to see resources from both VNETs regardless of which VNET I've established my VPN connection with since they are connected to each other?
For your issue, you can use connect VNET1 to on-premise with VPN, and connect VNET1 to VNET2 with peering, but if you want to connet VNET2 from on-premise through VPN, you have to set up gateway transit in both VNET.
You can finish you work following the document Configure VPN gateway transit for virtual network peering and you will get what you want.