A few points:
1) DynoJet's have the ability to do load bearing mode or Inertia mode for determing the RWHP of a vehicle. Load bearing mode is the same way that a Mustang Dyno determines RWHP. DynoJet's have had that ability for quite a few years and those that don't, it is an upgrade the operator/owner can purchase...
2) Mustang Dyno's when setup correctly will show a lower RWHP than a DynoJet in Inertia mode, they are generally the same when the DynoJet is in Load bearing mode. That said, it depends on the operator of the Mustang Dyno or Dynojet in Load bearing mode on where the RWHP is. It is very easy to show false RWHP numbers with a load bearing dyno such as a Mustang Dyno or DynoJet in Load Bearing mode. It is very easy for a Mustang Dyno to show higher RWHP than a DynoJet in Inertia mode. It is quite common for shops to show false gains...
3) To the OP, your dyno numbers will be meaningless if the shop does not lock the TC in 3rd gear, which means they will need to tune the EEC in your car. Since they are not doing any tuning, how do they plan to accomplish that?