Chromebooks have no such issue, because for one they are "browser-based" so ISA-agnostic, and two, Android apps are also ISA-agnostic for the most part. In fact the majority of native apps were optimized for ARM, not x86, last I checked, so if anything it's Intel's hardware that could cause some issues with some apps on Play Store-enabled Chromebooks.
As for performance, Apple's A9X can beat Core M on many workloads. A9X is probably no more than $35. That Core M was $280 (that's what the OEMs pay when they bundle them in their devices, possibly with some light negotiation).
http://www.extremetech.com/mobile/221881-apples-a9x-goes-hea...