I'm not denying that the difference might have been greater, but comparing prices of an 80D (all around current Canon tech except 4k), 6D (all around old Canon tech) and 6D II (all around current Canon tech except 4k and sensor), it looks to me that APS-C provides some great cost Potential for cost reduction. The 80D ist 900€, the 6D 1000€ and the 6D II is 1750€ on the german Amazon site.
Just because of the size difference, you will always get slightly more than 4 times as many APS-C sensors for the same material and production cost than full frame sensors. And you'll always lose less sensors at once when you have a defect in your wafer, increasing the yield advantage of aps-c further. How could that not affect cost significantly?
Apart from that, the M System is entirely different from the R System regarding its ecosystem. It is clearly all about size in contrast to R which seems to be all about image quality. Having the Option for something in between in the form of an APS-C R (less size thanks to crop, e.g. use a 85mm instead of 135mm and more IQ and ergonomics thanks to big glass and body) would nice in my opinion. If Canon thinks there are enough people that feel alike, we'll see an APS-C R.