I did some further troubleshooting and it seems the setting that is breaking this to begin with is the NTLM Pool.
If I remove it, I can move forwards.
But then I get a problem with NTLM:Disable function on iRule (on ltm log).
I changed it to ECA:disable and was able to move through.
But still I got issues when going to autodiscover. I see messages on ltm log complaining about HTTP:uri after response. I removed the iApp_login_timeout and owa_redirect_irule7 iRules and everything is working now.
I must be missing something, because the iApp is supposed to work out of the box.
This is BigIP 16.0.1.