In my experience trying exactly the same thing I found that it destroyed the tonal accuracy and compressed the sound causing what us old folks remember as the DBX expander effect where various tonal values are compressed or expanded unnaturally. It was, in my opinion just plain bad. It is possible to get some eq effect from Isone by moving the frequency curve. I frankly have not felt the need to add any eq. If you are experiencing some unpleasant or unnatural eq with Isone you probably have the Isone controls too far out of adjustment. Try using the natural crossfeed preset with or without CSC engaged to see if things sound natural. In that position it should clearly maintain the sound signature of your headphones and amp. If that does sound as it should then you can begin tuning the rest (HRTF). Using the room setting will add eq, it is supposed to do that to simulate various room acoustics. The room acoustics can be very useful in creating a natural sound depending on your source material. That is the value of being able to create your own presets.
Actually, I was using eq with the AD900s before ever using TB_Isone, because the phones have a too prominent high frequency response for me, particularly for classical music. So I just naturally kept it inline when I added TB. Anyway, I'll definitely take a closer listen to see what the differences are without it.
Having said that, I thought someone very early in this thread highly recommended using an EQ with TB_Isone, and even recommended certain settings for some of his phones, but I could be completely misremembering or confusing this with another thread.