I'm using it via the content server almost exclusively. I only connected as a wireless device when I cleared the data and had to resync the metadata for the books already on the device.
How Android deals with defaults - basically, if there's only one option, it uses it. If there are more options, it presents a list of apps you can choose from, and at that time you can select to make your choice the default. This is true regardless of whether you are in CC, or a file browser, or any other app trying to open a file or carry out a command. It is the apps themselves which "announce" to Android what files or commands they can handle. If an app does not make this announcement, one has to open files from within the app instead. But that's not the case here. Since Astro automatically opens the files in Moon+, that tells me that Android knows Moon+ to be the app for those files. It just isn't letting CC in on the conversation for some reason.
I no longer have any other reader apps installed except for Kindle and Google Play Books, and neither of those "announce" themselves as "file openers" - they both operate in their own universe. Neither have any defaults set.