Using Auto-target across differing markets

We have recently used Auto-Target and Auto-Allocate and by our understanding they both use the 'default environment' to build the model around hits and conversions(AT Overview). However globally we trialled running these tools on multiple markets in addition to our default environment, on conclusion the results didn't reflect any significance. We believe this is due to the model on running through our default environment and being able to differentiate between the other markets.

Has anyone been in a similar scenario where there is a need for multiple environments, but being able to run Auto-Target/Auto-Allocate through/bypassing the default environment to these other markets?