why don't you leave all your backups to automatically select proxies so you don't have to reconfigure them everytime, and instead you work with proxy configuration? The first thing that comes to my mind is to change the default processing mode of each proxy, and force each of them to do either direct storage or hotadd. In this way, virtual proxies will never be able to do directsan (unless your storage is ethernet based AND proxies have a route to your storage) and physical proxies on the other side will never be able to use hotadd. In this way, each proxy type will only process the type of storage it can see.
EMEA Cloud Architect @ Veeam Software
Veeam VMCE #1