I run correction, measure with REW and adjust all with 1 port plugged, eq 1. After everything is dialed in and I'm done calibrating I'll pull the plug and switch to eq 2 for the bump in mid bass output.
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Again, you have REW, so you know if it messed up with something else, nothing wrong with that because then you would do something else to counter any ill effects. The thing is, plugging and opening ports don't just change the magnitude of the output, it also affects the phases. When I say logical, I mean:
Let's say Audyssey created a set of filters based on the data collected with one port plugged eq1, call it filter set A, now after that you open the port and go with eq2 on the sub, so now Audyssey filter A will be dealer with the magnitude and phase response of basically a different sub albeit similar because it is the same sub just with altered FR and PR characteristics. So surely it would still work better than with no Audyssey EQ, but you can understand the results will no longer be optimum. Again, since you run Audyssey, if your don't like the changed outcome, you can do something else manually to bring it back to optimum, and still get the boosts due to the opened port and eq2. Also, by then you have reverted from targeting accuracy, to suiting personal taste.
It is like amplifier design, everyone has different taste, so the amp designer/manufacturer should design/build their amps for accuracy, and leave any customization efforts to the user. Same here with room EQ, EQ for accuracy first, and then make changes to suit individual taste. Just that it seems more logical for me to use the App because you can do a lot more than just opening a port and applying the sub's EQ that is fixed. As always, once individual tast/preference kicks in, ymmv will apply.
