I was having the same issue with the unlock, disarm and intrusion still detected. I sent a ticket and received the following reply from @karl “We should be adding delays to Smart Home Monitor soon. Also, when we add Smart Locks, that should be able to trigger events on it’s own.” Thanks for the update Karl!
On a side note, I did find a workaround. I had been using @ethayer’s Lock Code Manager [Depricated] Lock Code Manager which worked great except the alarm problem. I have since switched to @RBoy’s Lock Multi User Management with Unlock Notifications and Advanced Scheduling http://smartthings.ramitbhalla.com/ and it has the option to Disarm Smart Home Monitor built right in. This has worked without issue all day today. It does cost $10 to get the code but I liked the Thermostat device type and apps so it has been well worth the money.