If you read each individual school's questions for recommenders, it's clear that most of them ask more or less the same stuff. Thus, since my supervisors are busy people, I asked each of them to write a single, thorough LOR and had them send it to my undergrad university's career services office, where they keep letters like that on file. I then had the career office send them on to each school, all confidentially.
I called each school to which I applied to check if this was kosher. Kellogg was kinda queasy about it and Stanford said they'd really prefer their own form (or "matrix"). (I later decided not to apply to Kellogg.) I pointed out that their forms were pretty much the same as everyone else's, and that given that most applicants are applying to 4-6 schools, it was unreasonable to expect us to burden our recommenders with that much work (especially when we pay so much money for each application).
Duke and Darden specifically said that submitting a LOR in this way, in lieu of their "matrix," wouldn't be a point against me in admissions. As it turns out, I guess they were right. I don't see any adcom actually dinging you because you turned in a good LOR instead of their standardized form - they understand the position many of us are in. In the long-run, these schools really need to move to a standardized application format, as in other professional schools.