A case would probably have it back in spec, if its even out of spec on it's own. The energy is going to be so tiny in those high frequency waves because it's just signal and clock. Never mind that they are still pretty low frequency and those traces are going to be awful emitters in that range.
The highest energy part of the device is going to be the LEDs, which are switching well below the bottom of the standard EMI compliance range (10Mhz).
MCU outputs can be nasty with their high switching speeds. Every STM32 has some slew rate limiting as far as I know, but I looked at their code on GitHub and they're explicitly turning it off for most pins so I assume it's not an option for their driver ICs for some reason.
The highest energy part of the device is going to be the LEDs, which are switching well below the bottom of the standard EMI compliance range (10Mhz).