I have a variation on this scenario. When I do a 2x 20 min at FTP, I don't bother with Zwift, I am using the 1030 as a head unit to the trainer (Elite Direto). So I have connected the 1030 to the trainer, but I am using the Stages as the Power meter. This means, in theory, that the 1030 should be adjusting the resistance of the trainer according the measurement of the Stages power meter (I had set a target range with a variance of 10w).
The Elite Direto is calibrated with itself (using the Elite software), but it is not aligned with the Stages values, typically the Direto overstates the Stages values by about 20 watts.
What I have found is that while the Stages values are displayed on the 1030, it is not using those values in the adjustment of the resistance of the trainer. The resistance never hits the level required to achieve the target window - I think that this is because the trainer 'thinks' that the window is already achieved. I think the pairing of the trainer to the 1030 means that it uses the trainer, regardless of what is displayed on the 1030. If I disable the Stages, then the trainer's values are displayed and it makes internal sense. I don't do this because the Stage's values are what I am training against. The workaround is to select 'resistance' on 1030, instead of target power. Not great, because for each step you have to reset the resistance.