I would not say that the diffrence in stroke and bore between the Ktm 690 and 660 is that different:
Ktm 690 bore/stroke 102 x 80
Yamaha 660 bore/stroke 100 x 84

The rotating mass could be the big culprit. The xt has a huge wflywheel and probably a big counterbalance weight, and also a steel basket clutch. There could be a lot to win if one would reduce some of that weight but most often that only affect the free revving with no load.

I only did a couple of mods on my 2012 XTX, but already with full exhaust (homemade - i work with stainless steel pipes on a daily basis) and airbox mods (DNA stage 1 + 2) and Kev's fuel mod / or PCV it's a huge improvement.

I also do a lot of roadracing (race prepped SV1000N) and Enduro riding on a 2006 KTM 450 EXC so i know exactly what you mean. :)

I am doing some mild head porting and and fitting a stage 2 Hot Cam during the Winter on the XTX, and i think that will get me where i want to be in terms of throttle respose...
Going further that that, i believe will be a lot less cost-effective compared to just getting another bike.
As of now, i threw just under 750$ at the bike for the different mods, and that includes the complete Raptor 700 head i had to buy on fleabay to get the cam idler gears for fitting the cam to the XT head.