Curious… Of course, having the redacted debug file complicates matters, so you’ll need to tell us whether it mentions the correct SSID. If so, I think @sam_nazarko or one of the devs will need to explain how it’s (partially) working without there being a settings file.
Here’s my own settings file, suitable redacted, naturally 
Name=xxxxxxxx
SSID=xxxxxxxx
Frequency=2412
Favorite=true
AutoConnect=true
Modified=2017-03-31T11:53:11.063163Z
Passphrase=xxxxxxxx
IPv4.method=dhcp
IPv6.method=off
IPv6.privacy=disabled
IPv4.DHCP.LastAddress=192.168.xxx.xxx
Edit: Check out this post. It uses connmanctl to enter the SSID and passphrase.