As far as I know, free reed harmonics are in tune and I can't see any reason why they shouldn't be, since the sound comes from the periodic interruption of the airflow past the reed. Strings (especially piano strings) have out-of-tune harmonics because of "end effects" meaning the effective length of the string isn't the actual length (because there's some elasticity in the end points) and the end effect has different proportional influence on the vibration for harmonics, where the string is vibrating in sections.

The real reason why squeezeboxes are equal tempered is simply that many of them are fully chromatic and can be played in a wide variety of keys.

In fact, diatonic accodions two row anglo concertinas are no equal tempered, as both are restricted to a small range of keys and therefore can safely be in just (harmonic based) tuning.

Anahata