A chevy dealer told me the same thing after replacing tranny lines 2 months earlier. I think its bs personally. I think they don't want to do it because they only get like 60 cents on the dollar for warranty work from my understanding.
It's not bs, There are only 2 circumstances in which "crossline" warranty is permitted. The first is that you sold the vehicle used. The other is in an extreme emergency such as a weekend breakdown in your area. Some AVM's don't push it and some do. If it'a straightforward claim, it will pay. the computer doesn't care. If you submit for extra labor time or you are audited, the AVM has every right to deny or debit the claim if you violate policy and procedures.
For me, it comes down to risk benefit. Losing a tranny line or pinion seal claim? Oh Well. A set of injectors or head gaskets? I'll pass.