You answered your own question - it's about the legislation restricting emissions. The manufacturers could easily tune the engines for optimum power throughout their rev range, but their hands are tied, hence a market for power commanders and remapping ecu units.
Not a lot has changed from when you were tuning your old Nortons etc. It's just the technology is a little different.
Back in the day, if you fitted a free flow exhaust or high lift cam, you'd have to adjust the mixture by rejetting the carb(s) to provide optimum power (and most likely, prevent engine damage due to excessively weak mixture). The only thing that is different now is the way you adjust the mixture. Rather than change a mechanical object (jet), it's simply a case of altering the injector duration to provide a richer or weaker mixture as required. Much easier when you can do it via the electronics.
A lot of the tuning that is now needed is because of legislation controlling emissions and noise. As a result, many bikes (and cars) have less than optimal mixtures for power and torque at certain points in their rev range. Throw into the equation changing exhausts, air filters, cams and modifying heads and you'll certainly need to do something to correct it all. Build tolerances are much improved compared to older machines, hence one R1 being close to identical to another in terms of power and torque.
Take my V11 as an example. It has Mistral cans and crossover, a modified airbox, modified engine internals and a remapped ecu. Apart from the crossover, all this was done before my purchase, but changing from a std crossover to a Mistral made a huge difference to the engine power characteristics. It does run a little richer at the bottom end, has probably lost a couple of hp right at the top, but boy is it strong in the middle by comparison. It also needs to be remapped again to get the best from it, so a trip to the dyno is on the cards at some point. The last dyno print out showed 89bhp at the wheel with excellent power/torque throughout the rev range, particularly in the 3-6500 rpm range.
I don't think you'd be able to make massive gains on the engine to the top end power without major mods, but it's clearly possible to vastly improve the mid range without too much of a sacrifice at the top and extend the power over a wider band.
Hope this helps. Sorry for the lengthy post!
Trev