After letting this simmer for a bit I think I agree with you that boarding actions only cause the single possible crit, based on the wording like you said. My group has been playing it the other way, but it never made a difference (nobody's been rolling crits well recently).
Though I'd really like additional confirmation of this being the case, since I can't really justify the boarding critical rules replacing the normal "all damage causes crits on a 6" other than it being "intuitive" to play it as one crit roll per boarding action.
EDIT: It's the "regardless of source" bit on p14 that really gets me; without a specific, stated change to the contrary, it's very hard for me to dismiss "regular" crits from boarding results (on top of the special one). I'm surprised I can't find any threads on this issue in the past, I'm sure someone must have asked at some point...