As far as I can tell, there are two independent PGAs on the Teensy 3.1 chip; if this is true and there are no chip errata in the way, might want to update the technical-specs table here:

This is relevant for me because I'd like to use both ADCs in differential mode and with PGA enabled on both channels. At first I was a bit worried that this was not possible, or that a single PGA was shared or multiplexed among both ADCs, or something like that. (I haven't yet run an experiment with an actual Teensy 3.1 board to verify.)

See also Figure 3-32 in the reference manual, which seems to clearly show that each ADC has its own PGA.