The estabilished terminology is "architecture" for instruction set architecture and "microarchitecture" for the user-invisible implementation details. So, microarchitecture means for example AMD K7 vs Intel P6.
So the quote is saying that ARM vs x86 doesn't matter,
but eg Cortex-A8 vs Cortex-A10 does.
I was using paper as a basis since that's what is linked (which I found as a poor one)
"We find that ARM and x86 processors are simply engineering design points optimized for different levels of performance, and there is nothing fundamentally more energy efficient in one ISA class or the other. The ISA being RISC or CISC seems irrelevant."
So if you think as X and Y of course they don't matter. However we are talking about ARM vs x86 which have measurable properties in this whole discussions context+time, and that matters as "a phone powered with ARM" vs "a phone powered with x86" or "a server powered with ARM/x86". That's the level of terminology we are using.
So the quote is saying that ARM vs x86 doesn't matter, but eg Cortex-A8 vs Cortex-A10 does.