What is the reference chord for AoA measurement or calculation in a twisted wing?
In short: it’s up to the designer to pick any definition as long as the design and analysis always obeys that definition.

Usually, it’s a general practice to define a root chord and then calculate the rest of the local aoa‘s in relation to the root chord. This makes wing-strip calculations simpler. It’s also used in helicopter rotor blades and propellers.

On the other hand, there are numerous simplified calculations (that calculate wing or aircraft level properties) that may consider the mean aerodynamic chord. In this case, of course, the mac location would be used.