The differences are
(a) it may be out of tune: the chanter is designed to be in tune with a particular fingering.
(b) as PP says, ornamentation can be different.

For my sins, I have one set of pipes (Julian Goodacre's Leicestershire smallpipes) that use covered fingering i.e. only one hole open at a time; and a set of Jon Swayne pipes which are half-covered fingering. I'm beginning to find that it's dangerous to play the same tunes on both pipes because of fingering confusion, so each is developing a different repertoire.

That point about crossover notes is well taken. Not having previously been a wind player, my fingers are undisciplined in this respect, and I'm have terrible trouble with spurious crossover notes. I suppose practicing all the transitions as suggested is the answer.

On the Leics smallpipes, you are supposed to close one hole before opening the next, giving a small percussive burst of drone note (bottom D on mine) between other notes - quite a different technique and also difficult to get consistent. The same with Northumbrian, except that what you get between the notes is silence because the end is closed.

That's just about exhausted my knowledge on the subject. I'm still a rank beginner after three years!

Anahata