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Immersive Bass never removes deep bass (I've just measured it to make sure, it actually even adds a bit). There are no phase issues, not in the latest few beta's anymore (there were back when it was called Bassmathijzer). But, it's at the start of the chain, so it could be that things like Auto EQ, Bass EQ, multiband compressors and the bass clipper are pushing the deep bass down more if you add more warm bass.
Just listened to it standalone: You are right. It was just the standard settings that makes it sound like it does. I hear a lot of harmonic distortion on certain parts of music. For example on intro's where you only hear a (clean) kick drum. Setting the output lowpass frequency to 45Hz gives a better balance to my ears. These are currently my settings: