Are there benefits to either using the modem as the router and the TC in bridge mode or the modem in bridge mode & my TC as a router?
It's pretty much personal preference here. If you have a simutaneous dual band TC and you want to enable the Guest Nework feature, that would require that the TC be configured as the "main" router handling both DHCP and NAT services.....since the Guest Network option will not work correctly when the TC is in "bridge".
I've turned on bridge mode with the modem, but I'm still getting a double NAT error message with flashing amber light on the TC. What's up with that?
Sounds like the Zyzel gateway is not configured as a simple bridge mode modem. There are a number of modem/router or gateway devices that really won't allow a true bridge mode setting.....even though the setting might indicate that.
IF....the Zyxel really was in bridge mode, you would have to configure the TC to Connect Using = PPPoE credentials, not connect using DHCP or Ethernet.
When I reset the TC and restore all defaults, it comes back up automatically in bridge mode, is this normal?
AirPort Utility recognizes that there is a modem/router or gateway devcie "upstream" on your network and configures the TC in the correct Bridge Mode setting accordingly. This is normal.
When I try to turn off bridge mode, I get an error message about IP addresses, what is this about?
When you change the TC out of Bridge Mode, then it is acting as a router. So, you now have two devices on the network both trying to provide DHCP services (supplying IP addresses) and NAT services. IP conflicts are common when this occurs and it breaks a fundamental networking rule.
There are ways to adjust settings to reduce the chances of IP address conflicts, but you will still have an error known as Double NAT on the network.
Now, my Time Machine won't back up, telling me that the drive can't be found. Is this connected to my bridge mode issues?
Probably. The TC is confused now and has lost its way since you have made changes on the network. Once you get the network working correctly, you will likely have to reset the TC by restarting it and then possibly "pointing" Time Machine at the TC again as a backup destination. No sense in trying to do this until you get your network operating correctly again.
Bottom line here.......unless you are able to configure the Zyxel device as a "true" bridge mode modem, in which case the TC can only Connect Using PPPoE settings, you should reset the Zyxel back to its normal default settings of acting as a modem/router providing DHCP and NAT services....and...configure the TC in Bridge Mode to operate correctly on the network.
Or.....if it is important for the TC to act as the main router on the network, you might check with your ISP to see if they can provide you with a simple bridge mode modem......not a modem/router or gateway type of device.
As I mentioned earlier, your modem/router might have a setting for bridge mode.....but it may not be a true bridge mode setting.....as different manufacturers have different interpetations of what "bridge mode" might be.
Normally, bridge mode means that both DHCP and NAT are "off". The fact that you are picking up a Double NAT tells me that NAT has not been turned off on your modem/router....so it is not really in Bridge Mode.