I have downloaded and installed Citizen Sleeper (citizen_sleeper_enUS_1_1_3_57467.pkg) on my Mac where it automatically came with Episode 1 Flux installed.

However, in game it tells me to wait for Episode 2 Refuge but according to the store page it has been released at the end of October. Any idea on where to get Episode 2 and how to install it?

It's a late answer, but I think you will get the new episodes through updates ?
I bought the games some days ago and all three new chapters were installed.
So I guess, you only have to update your game to get those.

Have fun =)