I agree.

My issue was that the mute tended to give a deeper sound, I was going to say a lower sound, but I did not want to insinuate intonation. The deeper sound made it hard for me to actually hear it, maybe the sound waves? I switched to ear plugs because that hearing factor is not as obvious and I can pick out the intonation better.

The weird thing is that I play cello more, and am taking cello lessons, that low sound issue with the violin is not apparent with the cello, except when my cello is played with the rubber mute. But the cello without mute, which is what the violin with the rubber mute mimics to my ears, is not an issue. Weird.

I am thinking that I am used to hearing a violin as it sounds without a mute, and a cello as it sounds without a mute. A rubber mute on either one disrupts my ability to hear proper intonation easily. With the violin, it is mostly notes played on the E string with a rubber mute. With the cello, it is mostly notes played on the D string with the rubber mute. I have not noticed an issue with my viola either way. 

I prefer the ear plugs with the violin and viola anyway. My ears have always had some ringing. I do not want to make it worse by playing my viola or violin close to my ears without the earplugs.