I have sent in shorter bottles than the "standard" as long as the diameter is less than 2.75... you are good. As for Sam Adams, I have sent in entries to competitions in the early days that were Sam Adams with no issue... but cant recll if it was NHC or not.
In the end Sam Adams is likely ok.. but I would not send in one from any other brewery that had raised letters, as their limited distribution might make them "special".
That being said, I dont think competitin organizers are trying to exclude anyone over petty things, but keeping the size easy to put into cases, and not pushing the limits is always a good idea.