From development: The behavior is as designed and not a bug.
The Symbolic Math Toolbox (MATLAB side) uses a special definition of ~= which overrides MuPAD’s ~= . This means that MuPAD’s ~= no longer means “approximately equal”, but “unequal” like in MATLAB.
An easier example to see this is
which returns TRUE in MATLAB since 1 is not equal to 0, but FALSE in MuPAD since they are not approximately equal.