I have submitted update for iOS apps using 10.11 and Xcode 6 last week and they were accepted. Last year I submitted OSX apps using beta 10.10 (I had to modify a system file but it went through fine)You can't do that with El Capitan anyway. For submitting apps, you need to have it built on Yosemite or it won't send the archive to apple.
You can use a VM for Yosemite and have Xcode 6.3.2 running. Apple does not allow devs to submit apps that are running anything other than the stable releases of OS X