Talked to Wink support again, here's the scoop: so the 4 Zwave modes in the "hidden menu" are generic Zwave controls for adding & removing generic Zwave devices. This also includes shifting entire Zwave networks to & from different controllers. To recap, the 4 modes are:
1. Learning Mode
2. Shift Control
3. Inclusion Mode
4. Exclusion Mode
The first two are used to include multiple controllers in a Zwave network (controls can be hubs, gateways, remotes, etc.). They handle transferring network control between controllers without having to connect each device individually to a new controller. These are advanced controls and are not recommended unless you are pretty familiar with networking with Zwave. But this is cool because if you want to controls Zwave stuff on your Quirky network with say a physical Zwave hardware remote, you can do that, even though Wink is kind of a sub-ecosystem of Zwave that only uses Wink-Certified Zwave-certified products.
The second two are for adding & removing generic Zwave devices. Inclusion mode lets you activate a generic Zwave device and exclusion mode lets you "release" a generic Zwave (note: don't use this with Wink Certified devices; you're supposed to remove that from the individual product pages within the app). So Inclusion Mode basically activates the programming trigger in generic Zwave devices. As a reminder, the 4 basic control sets are:
1. BinarySwitch
2. MultilevelSwitch
3. GenericTypeThermostat
4. GenericTypeEntryControl
As Whackjack mentioned, you can get none, semi, or full support, depending on the device. For full support, buy Wink Certified Zwave (or other radio) hardware. The Honeywell thermostat is fully supported, but the Trane thermostat (made by Honeywell) has semi-support (does not support the "Auto" function). So once you activate a device, it shows up on the list of products that you can control
Exclusion mode is basically the button you press when you want to clear a Zwave device that has previously been connected to a network. When you press this, it removes all existing networking information from that Zwave device - it basically clears the network memory of the generic Zwave devie. Again, only use this button on generic Zwave devices, not Wink-Certified devices - you're supposed to remove Wink-Certified devices from within the product page.
So that's pretty much what the deal is with adding generic Zwave devices. It is possible, through a semi-hidden menu, but control is limited (only 4 types of control, based on generic Zwave communication commands) so it will be hit or miss as to how much device functionality you will get in a non-Wink Certified device. For best results, buy a Wink-Certified device, or read up online to see what level of success other people are having with generic devices.