Yes, simply include the mixer and preamp in the soundcard calibration test so that the negative response effects of the preamp and mixer are baked into the file.Is there a way to calibrate the mic preamp so that it can be eliminated from the effects?
The easiest to include is just the mixer with it's line-in and line-out ports, and you'll find that these line amps have the greatest effect.
The slightly harder task would be to include the mic preamp into the loop with the mixer. For that you need to construct a pad to lower the level to mic voltages. A 30dB pad is sufficient. The challenge is to shield the pad, so building it into the xlr would be best. You know if you did a good job by looking for noise in the files trace. I did this with my ECM8000 and Xenyx802 mixer and found the mic preamp compensation didn't offer much benefit compared to the messing around with the pad, but the mixer itself was beneficial. But, once the jobs done, you do have a more accurate cal file.
You'll still need to hold onto your standard loopback soundcard file though, to use if you want to test line devices responses.