It's not so much about capability of the hardware, more about the robustness of the design/development work done. What huge faults are you seeing in Toyota production vehicles? Every one I've drive has been pretty darn bulletproof from a calibration standpoint.
Sure, a standalone system has a lot of knobs to turn and that can be advantageous depending on your goals. Yes, you can tune based on IAT and MAP, but did you actually test it at all conditions or just extrapolate the map out and hope for the best? In essence I'm asking the small tuner shop if you have the time (or if your customer will pay for it) to turn each knob and optimize the system for all possible conditions? I do believe that any OEM calibration is a significantly more robust system than what an aftermarket/performance/tuner shop can produce in terms of reliability and driveability across a wide range of conditions. That's the bias I was referring to. For a racecar with a limited operating envelope I'd be running a standalone, but that's not what I'm building. Even street cars with fairly standard usage in a known environment can perform quite well with custom tunes, but we're talking about off-road, out-of-country overland vehicles here. It's a different demographic.
Custom tuning, standalone systems, etc is certainly a viable business model as has been proven by many shops. It makes sense when you're talking about performance builds because the factory systems do leave things on the table in the name of durability and conservative tuning for tails cases (ex: Joe Blow puts the s***ty 85 octane gas in Colorado in his turbocharged DI engine). This isn't a high performance build though, and the overland community doesn't seem to desire the last 5% of performance at the expense of reliability. The purpose of these vehicles is to take you across landscapes, altitudes, locations, and seasons without a hitch. Sacrificing some peak performance is a reasonable tradeoff for robustness to varying conditions.
My goal for this one is to drive it to Patagonia. That means huge changes in weather, altitude, and fuel quality. I want seamless operation in all environments (at the expense of peak power) so I'm relying on Toyota and their development process because it's far more thorough than what I can complete on my own. If I (or my customers) just wanted peak HP I'd just put an LS in it (and probably still use a GMPP computer).
This conversation has gone sideways.
I don't believe there are major faults in Toyota EFI systems in a stock setting. However, as someone else mentioned - there are issues with a 2uz ecu as they are set up for an A/T, not to mention you have to incorporate the immobilizer system as well. One of the most successful 40 builds I've seen, which was on here, utilized a 2uz - had to integrate the immobilizer plus use an A/T. This could be the shortcoming - where it 'works' with a manual but runs in a different mode as the trans codes are flying all over the place. This could snowball problems with power, reliability, and fuel economy.
I've seen 2uz swaps into ae86s with a manual, street and track driven, with stand alone systems. It's very possible.
I'm unsure what you think is needed in calibration variances. The purpose of EFI is to use a variety of sensors to provide information to a CPU that runs algorithms against base data to determine the fuel and timing. That accounts for elevation (map), throttle input, air and coolant temps, knock, and more accurate oxygen sensor readings (wideband if you please). A good system will even allow you to tune on the fly - which means you determine your desired outcomes and it will learn based on all inputs and real time data.
Tune on pump gas and you're fine - either stand alone or Toyota if you get gas with sediment or water- you're gonna have a bad time. There's nothing magical in a stock ecu that will fix that.
This is just a discussion, not an attack. If you get it all to work without loss of power, or CELs to ignore (I see that on "professional" 4runner 3.4 swap ads all the time - "CEL is on, but that's typical") then that's awesome. I would enjoy seeing this build succeed. I see others chiming in and wanting to see how you do it.
Trust me - I've been where you are (in a different manner). I had a 1990 Corolla set that had a 4afe engine - swapped to a smallport 4age, then used a JDM (ie - hard to find) 4age distributor, rewired the 4afe igniter to it, modified the 4afe ecu to run another 1300rpms. Was told by the community it wouldn't work - it did, for 9 years, and had the dyno to prove it worked and made more power. However, the dirty secret was that ignitors couldn't handle it (carried 3 spares at all times) and the ecu wasn't actually running right as there was no TPS signal (4afe was switch, 4age was potentiometer - no way to make it all work properly). Daily drove it for years and tracked that car. The demise of that car was a high compression (11.3:1) 7age build that the ecu couldn't handle. Looking back - had I just gone stand alone from the get go it would have all been better.
If you stand on the notion that factory engineering is nearly flawless to be suitable for everything, then throw that engine into another vehicle - you're throwing out the engineering that was married to that transmission, transfer case, diffs, engine bay, cooling system - meaning a lot of those re-engineered calibrations go out the window.
That's why we're all here.... to rebuild how Toyota did, or improve upon.