Rega Elicit-R Volumes: Phono vs Line

That is a normal condition. Amps sound better in the upper range on the volume control. I use this Schiit SYS to tone down the volume on my CDP to match the volume on my phono!
http://www.schiit.com/products/sys

I don't know about your amp's settings, but it is common for phono to sound quieter. That does seem like a lot of difference in volume knob position though. But maybe it is explainable. For starters the nominal target voltage for phono preamps was variable, but usually around 1 volt, while CD is specified as 2 volts, or 3 dB higher. Further, the "normal" output of a MM cartridge is around 5 millivolts, but your HOMC 10x5 is specified as 2.5 millivolts - perfectly serviceable, but 3 dB lower. Now we're at a 6 dB difference.

More difference could be explained by your particular recordings. For example, some recent Mobile Fidelity releases are cut at a noticeably lower volume than most other records. Or more probably, some of your digital recordings may be compressed to compete in the loudness wars. Such recordings can sound twice as loud as uncompressed recordings - think of the difference in advertisement volume vs. program volume on TV. 

Don't let me dissuade you from checking your setup, but you seem within the range of normal, at least in some circumstances.