This is Lavender Castle, produced by Gerry Anderson, who also did Thunderbirds.
Lavender Castle is a place of mystery and legend, fabled throughout the universe, a floating city of light, a place of peace, harmony and all the things that have ever been dreamt of. It is the centre of the universe and the greatest source of power - should it be destroyed, the universe would be plunged into darkness forever. Evil scientist Dr Agon plans to do just that. A lonely megalomaniac with technology-assisted powers of transmutation, he yearns for darkness and has pledged to destroy Lavender Castle from his fortress spaceship, the Dark Station, the most destructive power in the universe, crewed by unseen slaves working deep in the bowels.
In order to prevent this, Captain Thrice has set out on a quest to find the elusive Lavender Castle before Agon does and protect it at the same time. A previous encounter with Lavender Castle gave life to Thrice's walking stick and left the Captain with a special knowledge of its power and abilities. Travelling in his cottage spaceship, the Paradox, Thrice assembles a crew of misfits to join him in his quest, combatting evil wherever they find it as they travel the universe searching for clues that will lead them to Lavender Castle. But Lavender Castle works in mysterious ways and lends its power to the Paradox crew to protect them when they most need help.
Captain Thrice indeed looks like a garden gnome. Isenbard the engineer wears blue coveralls and has a Scots accent. Lyca has butterfly wings on her helmet.
I found it with a search of "stop motion" tv series alien crew scots accent, which brought up this list, and I started searching the names of items listed as stop motion.
The first episode - "In the Beginning"
You can see Dr. Agon's trumpet weapon in use in the episode. It shoots red blasts that burn and strike with concussive imapct.