The problem with playing FoS on the pipes is that it wasn't written for that scale. The flattened 7th (I'll take your word for that by the way) can only be represented on the pipes by playing what we pipers call a C natural, basically a flattened C but not a C flat, which is of course is a B.

The C natural just sounds like you've played a bum note, it doesn't sound all that good at all, so I think most of us play a normal C because it's the lesser of the two evils. It's not their fault, it's just not a pipe tune, not a Great Highland Bagpipe tune anyway. Great song though!!