I guess I'm missing something regarding the necessity to "change outputs" for the test signal. There has to be a way (even if it involves creating a distinct PRIR for each speaker angle) to use the same analog output.
Please see the manual on p. 37ff and 62ff on creating a PRIR sound room.
You have to assign a speaker label (L, R, C,...) to a channel number. The test signal for that speaker is then output through that channel.
So if you do it in one PRIR, as Got the Shakes described, you have to reconnect the amp to the new output channel for every speaker. So you star by measuring the L spesker with the amp connected to analog out channel 1 on the A16, sit in the chair, measure your look angles, then press BACK, then you have to reconnect the amp to channel 2 (and I think also go to the speaker select page and unselect the L speaker and select the R speaker, Got the Shakes may correct me here), then sit back again on your chair, rotate 30 degrees and do your measurements for all your look angles (however you do that when rotated away from the center looking position) for the R speaker, then press back, reconnect to channel 3, and so on, up to 16 times...
If you do it with one PRIR per speaker, if that's possible, then you maybe only define a new PRIR sound room for every measurement where you assign every spesker label to chsnnel 1, if one can assign every speaker label to every channel! Since you can only define two PRIR sound rooms in parallel you have to go to that menu many times to reassign spesker label to channel 1 to create a new sound room for every speaker.
Theoretically you can do the latter method w.o. leaving the chair. But if you're rotated facing away from the Realiser you'll have difficulties looking on the display, and this is necessary for changing options because the web interface isn't implemented yet.
When creating the listening room later on, as far as I understood only the spesker lsbels are important, not the channel number with which it was recorded.