I came from a wonderful FJ62 with a 3FE, so yeah, comparatively, the 4.7L V8 is awesome..... but, it is in a 6000lb rig.....
Mine is also a 2006.
I don't know if the VVT is super tough to tune or why no one mentions doing much with the later models.
HFDPNL- Having owned and built several turbo and supercharged cars and more than 40 engines, I would say your mechanic is full of ....... stuff. Unless You are rebuilding with upgraded pistons with lower compression and better rods, You are just throwing money away rebuilding most Toyota engines at 120K miles.
My bet for my engine if I turbocharge it like I hope to, will be to install a water injection kit, run larger injectors, and because I am moving to Colorado, I may look into E85 fuel usage and a tune for E85 and one for premium fuel with water injection.
I have also looked into running some extra thick Cometic Head gaskets and some ARP head studs before I have any problems.
I just don't know if I want another daily driver hot rod..... I have had so many and truthfully, I wish there was an easy factory solution for this rig to add 100hp.....
TRD does a great job on most things, it is a shame that they did a band-aid on the 4.7TRD supercharger fuel and ecu.