I upgraded to Mac App Store Core Tunnel today. I imported my configuration from 1.1.2 and all my connections are correct. I set up sync with iCloud.
Several of my connections are the same on different computers, but I use a unique key on each computer. When the configurations sync with iCloud, the most recently used private key name is used, which is not correct for each computer. I have to manually change the key on the connection I want to use which then syncs to iCloud.
My humble suggestion would be to disable this by behavior all together as I believe it would be more secure. Alternatively, you could have an option in preferences to disable this behavior.