Min- burn times of 5-7 minutes are not an issue for low-mass boilers. The average time doesn't matter as much as the minimum time, and the number of burns per hour/season. If it's chattering away most of the day at 10 burns/hour on zone calls, the 200+ burns per day is a bit on the high side at any length. But if it's no more than 5 burns/hour under the worst-case conditions, and under 100 burns/day, it's not going to suffer much. With sufficient buffer to guarantee overlaps with 3 burns/hour or less you can microzone the place to nth degree without any concerns.
I'm not sure how you're getting 5+ minute burn times out of a mega-microzoned setup though. The very rare house that really NEEDS an Alpine 150 at Andover's 0F 99% outdoor design temperature would have to be pretty large (7000' +) or fairly leaky/lossy (say, an antique solid masonry building with no insulation). It's min-fire output at condensing temps is about 28,000 BTU/hr, and it takes about 130' of fin tube to fully balance the output with load at 120F average water temp (about the lowest you can go with fin-tube and get consistent results with outdoor reset modeling). If you don't have at least half that on your smallest zones there's some potential for short-cycling. But if the micro-zone calls are always overlapping and you never see 5 burns an hour, it doesn't matter that much.
To be sure during the beginning of this season to date it's likely wouldn't need output any hotter than 125F to meet the load, and if you haven't tweaked in the outdoor reset curve yet now is the time to get started.