I'm an old fan, so this was a long time ago, but I think it was an interview with Hiroki Hayashi, the director and co-creator of Tenchi OAV1 and likewise for El-Hazard, in which he said that he gave complete control of TM!R to Masaki because it was his baby, and that El-Hazard was basically Hayashi's own version, hence the similarities.
This wasn't in the interview, but maybe the harem ending was where the creative differences came in?