At least for gondolin and microsandbox, you bind a specific secret placeholder to the target host. i.e. your GH token is only replaced/injected for calls to api.github.com, not other hosts. And you can set up both with deny-by-default
Only if the replacement is global and not, say, only looking and inserting it into the actual (eg) Authorization header. If something is only transparently altering the Authorization header, then an agent inserting the dummy value somewhere else is totally safe.
For clarity, there is no "search and replace" function going on. It's only setting the header.
The main reason a "proxy-managed" env var is set is because most CLI tools assume if the env var is set, auth is set. If the env var is unset, it will assume auth needs to occur. Fortunately, most don't do a pattern matching on what the value actually is.
You just don't inject the real secret unless hostname/whatever rule matches the request, right? I don't know if that's how this works but it's my assumption.