For those of you in the future who may be looking for an answer on this issue (low gain after calibrating the SU-R1000 phono EQ), this was a combination of poor manual instructions and user error. Apparently if you are using a LOMC you must set the +3dB gain to “on” before running the calibration. If you calibrate and THEN try to turn the gain on, it defeats the calibration settings.
I did go back and set the gain to +3dB, and turned the volume on the amp way down before re-calibrating with the LP and the phono pre and line level inputs are MUCH closer. Plus if I want them to be practically matching there is a setting to attenuate the Line In inputs to get them almost level.
This was very helpful when trying to compare the phono pre in (vinyl), my NDX2 DAC (line in), and the internal DAC (USB in), getting the levels between inputs much closer and eliminating the noise floor on the phono pre input.