There's no real way to tune the OEM ECU, yet, in the way you are thinking. Seems like HP Tuners has some Toyota compatibility but it's nothing the availability for GM products. There might be a piggyback from URD or Unichip but I haven't looked. The supercharger flash from Toyota for the TRD supercharger was irreversible. I'm not sure if it's the same for the Magnuson or Procharger tune.
Like everyone else said, until there is a consumer solution that lets you reflash parameters on the stock ecu theres really not a lot to tune. A local shop could do a dunk test on your 4Runner to give you HP and TQ read outs but that’s about it.