Starting multiple HomeBrew Services
First, you are not able to use brew service to start the two different mongodb. Cause the LaunchAgent .plist files have the same name. The former enable one will be overwritten by the latter one. Find the corresponding .plist service file, copy it to ~/Library/LaunchAgents as a different name.

Secondly, the service .plist must be modified to use a different conf for mongodb. It's impossible to make two daemons listen on the same port.