Use Cases:
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Automatically unlock upper lock when lower lock is opened by keycode? - Yes this can be automated by either coding it yourself to subscribe to the door’s unlock event and fire the unlock event on another lock, or you could use something like: Simplerulebuilder - now private to generate a rule.
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that this chain of events only happens when the lower lock is opened by keycode from outside - Yes, that should be possible though you may need to alter the Lock Code Manager code to do this rather than using the rules engine simply because you are listening for specific codes/users to unlock.
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Can this app or anywhere in smartthings tell all my house locks to unlock in the case of the fire alarm going off, if it is an integrated smart fire alarm, of course. - SmartAlarm can do this.
I am not going to try to sway you in any Hub direction, I came from HomeSeer which is not a route I would recommend any longer. Personally I love my ST hub because I am a tinkerer and enjoy the ability to create anything I can imagine. The code structure is easy to learn and manipulate and all device types/smart apps are editable.
I would say the major pitfalls I have seen is cloud performance, and documentation. By cloud performance I specifically mean the delays that have occurred on and off over the past few weeks where it may take a few seconds or minutes for a command to process but I believe these are being addressed. Documentation for programming is done but there are many advanced features available that are not documented properly yet.
If you do go the ST route and need some help coding, just reach out, will work for beer if you want me to code it up for you 
Or there are plenty of people here including myself that will step you through coding it yourself.