Ok I will chime in here being I have worked for a Subaru dealer as a Service Writer for almost 4 years, before going back to Toyota and been in the industry for 8.
1) SOA and only SOA can deny a warranty claim if modifications or abuse have occurred. A dealer does NOT HAVE AUTHORITY TO DO SO!
They can deny a warranty claim if the problem is not within coverage or the problem is not a defect( a cracked windshield or a gouge in a seat cover).
2) I have asked this very question to my old DPSM from SOA and he said yes they can detect if a vehicle has been reflashed with the Subaru Select Monitor 3. There are a few function tests that the SSM3 can perform on the ECM.
I have also heard that it compares calibration ID's for the ECU verse what it is supposed to have, but have yet to test this. I have heard that the old Subaru Select Monitor version can not detect this.
3) Folks, keep in mind that there has to be a reason for SOA to need this kind of info. Half the time we can tell if the car has had mods and it was returned to stock. This usually includes bolts missing, fresh wrench marks on the bolts, bolt marks where the bolts used to be but now in a different location(usually on heat shields, etc). I have never ran into a single instance where the car was returned to stock so well that my DPSM requested us to check the ECM.
I will say this though. If you are honest and up front with us, you will have a far better chance of getting coverage. Those that tried to hide it, always got it denied as nobody likes to be taken advantage of and this includes an auto manufacturer.
If they find the ECM has been reflashed or there are enough engine modifications found on your vehicle, SOA can remove the powertrain coverage. I have seen it done a few times. Every dealer that runs a VIN Inquiry will see all the notes and title info on that vehicle which includes notes from any DPMS if they removed coverage.