loaded language like "crippled" isn't going to convince me of anything... you pay for what you think the functionality is worth. what is physically there is of no importance at all. it's only what it DOES that matters.
it's not irrational. it is perfectly standard practice throughout the whole of the technology industry and has been since forever. (in fact it is not just the technology industry, but because you can't "see" what the hardware can do they have a lot more freedom to do it.)
If you think €57 is a fair price for 16MHz and 9Mb, then pay that much and get that much. If you think €107 is a fair price for 28MHz and 63Mb, then pay that much and get that much. It's as simple as that.
It especially makes sense because the actual components cost pennies compared to the R&D and the tooling. The one-off costs dwarf the per-unit costs for small runs of anything, so it becomes even more important that you maximise volume.