I tested this with 2.9.2 beta and it seems to be fixed when baking with cpu device, but baking with GPU using CUDA caused the result to be too dark.

I was able to replicate the problem and narrowed it down to being caused by a subsurface scattering shader node which is not connected to the active output. Also, the problem doesn't occur if the alpha blend mode in Eevee is set to Additive or Multiply, or if the subsurface scattering node is connected to the active output via a mix node(even with fac set to 0 fixes it).
Seems like having the subsurface scattering shader node present but not connected causes something to go awry, maybe with z sorting and or viewport updates of the material.