if the master cylinder is a smaller bore size in relation to what was originally spec'ed with the calipers then yes the pedal will feel softer. Basic hydraulics
Yes you have more hydraulic force but the actual surface area is the same and with the same rotor the leverage on the wheel is the same. The piston diameter in the caliper is multiplied by the rotor diameter, number of pistons and friction, so an ~8mm increase in piston diameter (4mm difference...
The 86-95 4runner calipers that are being referenced a lot in this thread are not a bigger pad, at least not in any meaningful amount. Just a bigger piston.
I’m not sure why there is discussion about wheel and tire availability, there are dozens of OEM Toyota 16-17” wheels with deep backspace...
Bigger calipers grabbing the same rotor diameter isn't an upgrade. any noticeable difference from this is simply from fresh parts and fluid.
If you really want a upgrade in stopping power, you could do the 00-06 Tundra brakes (~12.5" rotor) or 2010-up 4runner brakes (~13.5" rotor, honestly...