I don't think any TV viewers or people at the ground were unable to tell the teams apart, however it would have provided a visual hindrance to the players and there is no need to have both teams wearing the same colour shorts / etc.
I think anyone who has played League, OzTag or Touch knows that at times, especially in broken play, you don't have the opportunity to get anything more than a partial view of the people around you (especiallyin broken play). If both teams are in black shorts or have similar jerseys, it increases the chance of a pass going to the wrong person or opportunities not being taken.
Now I'm not suggesting that Cody Walker's pass went to a Penrith player because of this, but there is a risk that plays could have been impacted by something that was easily avoidable.
For me, I don't know if Souths need a full alternate (although they were happy enough to have one up until 2019), but they should at least base their black & white versus of their primary based upon their opposition.