Hi,
Normally, when we establish a VPN connection, we will receive the DNS setting from VPN server.
Windows client will prefer the VPN connection's DNS setting by default.
>>I verified this by making sure that the VPN Connectio GUID is on top of the list of the HKLM/System/CurrentControlSet/services/tcpip/Linkage Bind REG_MULTI_SZ value
If your binding order is correct, it should work for you.
As a workaround, we may try to configure NRPT on the client to force your client resolve the company's domain with the internal DNS server.
https://technet.microsoft.com/en-us/library/ee649235%28v=ws.10%29.aspx?f=255&MSPPError=-2147217396
Note: This article is applied to DirectAccess, in your case, please start with step4 by using local group policy.
Best Regards.