I used to rebuild starters, alternators and generators for many years. If you wanted higher charging voltage, we installed a Transpo higher voltage (14.7+v) regulator or an adjustable voltage regulator depending in the alternator.
I can wrap my head around how that harness ups the voltage after the regulator.
There are a few possible options.
Custom alternator built for higher voltage. Get a good known brand, like Optima, battery tender that has the AGM charge option and charge the battery a few times a month.
With the 3rd Gen Tacoma you can get a tuner to up the charge voltage through the ECU since that is what controls the alternator charge. I don’t know if that is the same for the 5th Gen 4R.