Gecko's run was on a Dyncom dyno and yours a Dynojet. To make for a more apples to apples comparison, I would compare Dynojet runs. Plus, it's been my experience over 25 years of racing, modding, and dynoing cars that Dynojets tend to produce the most consistent numbers as the way the machine operates and calculates power is extremely simple plus the Dynojet corrects for atmospheric conditions.
A 28% drivetrain loss would be unexpected, even for a 4runner. My RWD 6MT BMW M235 has a loss of around 12%. Given that the 4runner is RWD, but spinning through a transfer case, and heavier wheels/tires, a ~15% loss would be more likely. I could see ~20% in 4HI or 18% for a 4runner Limited that's spinning through an AWD-like system.
The Dynojet runs I've seen for stock 5th gen 4runners show ~230whp and ~240wtq. Assuming a 15% drivetrain loss when running in RWD mode, that calculates out be very close to the advertised power of 270hp/280tq (divide the Dynojet number by 0.85). Per the link below, this stock 5th gen 4runner saw 231whp/237wtq. We know Toyota doesn't underrate or overrate their power numbers except for the new Supra which is severely underrated since it's basically a BMW and BMW severely underrates their power numbers. Usually what's reported as the flywheel power is close to the power made to the wheels on most late model turbo BMWs.
Should you Supercharge your 4Runner? Magnuson Supercharger Review
So, for your dyno, it looks like around 356hp and 335tq at the flywheel or about about +86hp and +55tq over stock. I also agree with you, your truck would have likely seen more HP and TQ if could be revved another few hundred rpms. I'd bet 10-15whp/wtq is missing.
Procharger advertises a 40-45% gain over stock with their standard kit for the 5th Runner. They're pretty close to their claims. Your 4runner could have been heat soaked which could account for slightly less power plus the matter with the stock vs new redline.
2020-2010 4Runner (4.0) | ProCharger
Admittedly, the Procharger powerband is better than I was expecting.