Looking at the caravan test harness I see multiple independent ground connections. Can someone explain to me how this works?

The ground domains are probably all tied together through the substrate somewhere. However, the substrate being relatively high resistance, the connection that matters is off-chip. VSSIO is the primary ESD ground and ground for most of the pad-facing circuitry in the padframe. VSSD is the digital ground for the management SoC. The VDDA/VSSA domains are for analog and they are not really tied to anything other than some analog switch circuitry in the pads, and VSSA is in a deep nwell pwell and should be pretty quiet. VSSD1/VSSD2 and VSSA1/VSSA2 are the user area digital and analog grounds, but they aren't tied to anything until you connect them to something in the user area. So all of them should be pretty quiet. However, again, the VSSA lines are rotected by deep nwell regions while the VSSD lines are connected to VSSIO through the substrate, so use VSSA if you want a quiet ground. Each of these lines has a corresponding padframe ring (or part of one). In caravan, you can also ignore all of the existing ground domains and use any analog pin as your ground return.