Oh yes, sometimes you actually notice this, often when approaching a certain note from above and below. Depending on the harmonic function, the major seconds are not always the same size and you end up singing out of tune.

So, one always tries to understand the harmonic function of the choir as a whole in relationship with the structure of the piece. For example, if tension is needed, one can sing even more towards a dissonant diminished fifth. Close harmony is all about that.