I don't see anything wrong with having two compositions by Chopin as long as one of them is an etude. Chopin etudes are basically the gold standard (Juilliard requires two etudes: and one MUST be Chopin). If you have a Chopin piece as your major romantic work, I see nothing wrong with that.
For something as small as having an etude of Chopin and a scherzo, I'd say to focus more on how you're playing the material than what you're playing.You could play a Liszt etude, sure, or perhaps a Schumann etude, but if you play them horribly, you're far better off playing Chopin.
if one is exceptional enough, it hardly matters, but in a very competitive scenario, and with a subjective panel, it can make a difference sometimes. 'know your audience, and 'know the competition' are key things to keep in mind in these scenarios.again like you said, it's 'ok' and all, but it would depend on the above for me if i wanted to 'risk it'
It's a really good program. Some people on this forum will likely say that it is very unadventuresome and safe, but your program is very good for auditions to most schools.