Great question paullb,
I own both of them, therefore the following comments are based on long term listening in the same system. The Motherload MKII and Rhythm 1.4 are at the apex of the state of the art in tube based line-stages. Both are built/designed by very talented artisan craftsman.
As I stated in my review great tube preamplifiers completely disappear and totally allow the tubes to be heard along with providing the necessary dynamics/speed of the music by having superlative power supplies.
Therefore, the difference between the two line-stages is which tubes they use. What do you like better, 6SN7s or 12AU7s? Both tubes are great, but present music somewhat differently. For example which do you like better 2A3s,300bs,211s? All great sounding power tubes but different. Which would give you more synergy in the context of your system and better fit your personal taste? Both preamps are superlative, but different because of the tubes they use.