Inserting a note or indeed changing the arrangement of movements would help rectify the issue.The publishing house of Peters has inserted a note in existing copies of the score explaining the situation.
[This is indeed the same publication in the Main Wiki.
In terms of the general community, what do you think works better? Andante or Scherzo second?
In my opinion, both have problems.
If the Scherzo was second:
The bombastic harshness prevalent in the orchestration and thematic material remains very similar for both the first movement and the second, because of this I believe it is weakened - the material is blocky rather than more spread out. That said, the key signatures of the movements make more sense with the Scherzo second. The A, A, Eb, Cm-A fits easier, because of the c minor introduction to the last movement acting as a key signature bridge.
If the Andante is Second:
The opposite of above, the similar material doesn't encompass the first 40 minutes of the piece, rather having contrasting material in between. However (again opposite of above), having the first in A minor, then a sudden jump up a tritone to Eb and then back again to A is a big ask.
All in all I agree with the Allegro - Andante - Scherzo - Finale, as I find the material more important than the key signature fluidity.