I have an openvpn access server setup running centos. I've allowed all my private subnets access from vpn clients, as well. A lot of people connect to the vpn on the internal network as well, which is fine, but I want to change the preferred route when connecting internally.

Basically this is my issue: 10.1.2.1 is becoming the gateway because that is the range assigned by the OpenVPN access server (10.1.2.0/24) when connecting to it using the client. When connecting from an internal IP address (172.16.0.0/16) it's using the 10.1.2.1 gateway as the preferred route to an internal server, as opposed to using the gateway 172.16.1.1 (internal gateway). Is it possible to change this routing behaviour so it uses the 172.16.1.1 gateway as the priority? Is it possible with the access server web admin or another way?

It sounds like the server is redirecting the gateway, it is one of the configuration options. If you disable this behavior, a route will be added but the gateway would stay the same. In same cases this is preferable, it's really up to how you're using it.

Generally, with the gateway redirected, all traffic would pass through the VPN once connected. The alternative is only traffic to hosts on the VPN passing through the VPN. (I'll admit it's been a while since I've configured OpenVPN)