Well you've altered the original nature of the car. Hence modifying it. If it wasn't a registered fitter then (I'm not saying you have) the safety of the could be compromised if it hasn't been fitted properly. The alarm in my Mk2 hasn't been fitted correctly and the bastard thing goes off anytime it wants - making it a hell of a lot more noticeable in a car park - and then it doesn't go off when it's armed and you open a door.
Will be getting my 6i606 fitted by an thatcham approved fitter when i get around to it.
From an insurance perspective, I can see why they'd put the cost up.