I completed a masters prior to applying to Ph.D. programs. I used two referees from my masters, and one from my undergrad. The reason I decided to obtain an LOR from my undergrad advisor is precisely the reason you mention above: "admissions committees want to hear positive remarks about all stages of your academic training." In my case, it was to establish that I had developed an approach to scholarship, while in undergrad, that I continued at the graduate level.
I was successful in applying to programs, but, of course, I can't say the undergrad LOR was the reason, only that it didn't hold me back.