Right now this is a limitation of the program and MSTS. The reason is, locomotives must be differentiated from "wagons". So to know if I'm dealing with a locomotive, I use either "DIESEL", "STEAM" or "ELECT", or "ENG~" if it is a missing locomotive of unknown type. AM doesn't allow any other type classes for locomotives.
As I said in my response to your email, you can use the "Rolling Stock Groups" capability to accomplish what you're trying to do. Just put all your BNSF equipment in a group. Note that any piece of rolling stock can be in multiple groups at the same time.
For a future release I'll see how I can get around this limitation. I am thinking about a major update to Activity Master, like I did to Activity Generator with AG4. It would be AM2. If I tracked whether something was a locomotive (which needs the "EngineData" tag in the consist or activity files) or a piece of rolling stock (which needs the "WagonData" tag in those files) separately, then I COULD allow you to set types for locos. Even have types for 6 axle vs 4, modern diesel vs transition era, different railroads, etc.
The advantage of my allowing all this would be you'd have a lot more control over what replacements are made. The disadvantage is that would be a lot more work to set up.
One third option: use the "Specific List" option (click "Specific List") when replacing so you only replace locomotives with the era, railroad, and number of axles that you want. That's the way I do it, so I don't get 4 axle Geeps trying to do the job of an SD75MAC etc.
Thanks,
Steve