By chance, is the TRD running a different OD tire? That alone could be the reflash, esp with regards to tire revs, resulting rpms, shift point algorithms, etc. Also different markets with different fuels etc....you said it shifts better. Major OD tire changes have multiple affects.
If the stock intake is the bottleneck, opening up flow can have major issues too. Very common on Toyota motors I have dealt with in Lotus world. 2ZZ and 2GRfe. CAI was a real PIA to develop. Radium screwed up badly on the 1st NA version of the Evora....Sure big HP boost, but the shape overaccelerated airflow, could cause CEL and a few motors detonated due to lean burn. I had a Radium..sold car with no issues.....lucky I guess.!. With a simple CAI and Larini exhaust, you could go from 276 to ~just shy of 300HP....no other tuning. The relation of intake and tranny shifting on Toyotas are another PIA to contend with in tuning world and was experienced with Evora 2GRfe and IPS tranny. So your reflashes are no surprise to me at all....but numbers WILL NOT be identical.
GR8Santini, being honest, when you said no carbon issues with DI, it revealed a glaring misunderstanding of motors. DI injection makes power but without sideport injection that wash the valves, the motor is destined to fail with carbon issues. Do some research on the profoundly shitty motors in most Volkswagens!!!! They are about as bad as it gets....therefore, carry that over to all VAG motors......its been a quietly hidden achilles for years. Porsche just hides IMS issues...hehehehehe...germans never make mistakes my as$!
LSPI and our new SP oils are specifically designed to address these issues. Valvoline Restore and Protect is a new paradigm in motor oil. Everyone else is playing catchup. I have witnessed it firsthand. It has released a ring on my 4C that never burned oil on street, but would eat a quart on track. Monday it burned NOTHING!!! All within 200 miles!!!
I am not an offroad guy, but my years on track have given me a different perspective, ironically with Toyota motors over the past 20yrs. Camry made 268 HP, Evora made 276.........see numbers not same......even a few parts change the numbers....