Is there a reason the primary base station (which in my case is a 3tb time capsule) has to be connected via an ethernet cable to my modem (which in my case is as well as being able to connect via an Ethernet cable is also a wireless modem)? Can't the primary base station connect wirelessly to the modem and then wirelessly to the second airport extreme?
No it can't, not if you want your TC to be a router or an extender. The TC cannot extend a WiFi network that isn't an Apple network wirelessly. No router can route wirelessly, for many technical reasons.
Put simply, Ethernet is more reliable and faster. If you can use Ethernet, use it.
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