So does Ford engine dyno with the exhaust or do they wheel dyno?
If they engine dyno, it seems weird they'd do it with the whole exhaust system as well. If they wheel dyno, as I stated earlier, the R is going to have higher hp and torque numbers because the drivetrain is different. Resonators would probably be a very miniscule effect, but wheels that are 17 lbs lighter are going to give higher HP outputs on the rollers and slightly shorter (artificial gearing) are going to result in a bump in torque as well.
Among the many tests Ford does, one of them is to test to the SAE J1349 "Surface Vehicle Standard" that (in essence) measures the power for a given engine. You can pay to obtain the results from SAE. For example, you can find out more about the 2018 Mustang GT SAE test from here...
CPFD1_18MUSGT91: J1349 Certified Power Engine Data for Ford as used in 2018 Mustang GT 91 RON - Level 1 - SAE International
The procedure has room for differing test methods. A “fully equipped” engine is required for the net power and torque test and that includes the exhaust system.
https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0ahUKEwju6IbX2vTbAhVwuVkKHfj2AmMQFggpMAA&url=http://www.mie.uth.gr/ekp_yliko/SAE_%CE%94%CE%A5%CE%9D%CE%91%CE%9C%CE%9F%CE%9C%CE%95%CE%A4%CE%A1%CE%97%CE%A3%CE%97_%CE%9C%CE%95%CE%9A.pdf&usg=AOvVaw0cTiFJiy7xKBVUb8K2_3IR
A complete series production Exhaust System (including mufflers, active catalytic converters, resonators) or any laboratory system that provides equivalent restriction at the peak power engine speed. If a complete vehicle exhaust system is not used, the laboratory system must include the vehicle system at least through the first major restriction (e.g., close-coupled catalytic converter.) It is strongly recommended that a full vehicle exhaust be used with four-cylinder engines that are typically most sensitive to exhaust system tuning. Procedures for determining application specific exhaust backpressure are given in section 9.
For transient vehicle testing...
9.1.1 VEHICLE EQUIPMENT
The test must be conducted with a vehicle matching as closely as possible the intended design for series production. Exhaust system and charge air cooler design and engine mass flow must match production intent. Slight deviations are allowable as are typical of pre-production parts.
9.1.3 EXHAUST PRESSURE MEASUREMENT
Instrument the vehicle with pressure probe(s) installed downstream of the exhaust runner collector for each exhaust manifold. The same method and location of exhaust pressure measurement used in the vehicle must be used in the subsequent dynamometer net power test to set exhaust backpressure. For turbocharged engines, backpressure must be measured downstream of the turbine.
9.3
Application of Vehicle Transient Data to Net Power Test The exhaust backpressure, charge air cooler parameters, and engine control parameters shall be determined by averaging the transient vehicle test data for all test runs. The dynamometer net power test shall be controlled at each speed set point to the averaged parameters recorded during the vehicle test. The exhaust backpressure applied to the dynamometer net power test can be set with a valve or orifice plate sized and located to match the average vehicle transient backpressure at the engine's peak power speed.
Here's an example of a J2723 test procedure done.
http://www.gmpowertrain.com/PowertrainFiles/Engine/Plots/Insignia_Buick Regal gas LHU.pdf