Web App that point-to-site to VNET1 cannot connect to VNET2 which has VNET-to-VNET with VNET1

Hi, 

I have two VNETs environments, VM1 located at VNET1 and VM2 located VNET2. I setup a VNET-to-VNET connection based on Configure a VNet-to-VNet VPN gateway connection using the Azure portal document. the VM1 and VM2 can communicate to each other without any problems. 

At same time, I setup a Web App with App Service Plan(Standard plan) which connected to VNET1 via Point-to-Site connection by following Integrate your app with an Azure Virtual Network. From Web App's kudo console, I can tcpping VM1 without any problems. But no matter how I did, I just cannot tcpping any port on VM2. I am not sure if I need to setup a route. If I do, where can I setup that route? Can anyone point me how to achieve that. 

Everything I did was based on Resource Manager deployment. 

I also tried to setup peering between VNET1 and VNET2. As long as I configured VNET1 to use "Allow gateway transit" and VNET2 to use "Use remote gateways", Web App is able to communicate to VM2 located on VNET2. But I am just wondering if I can do the some things for VNET-to-VNET situation. 

Thanks.