I'm currently looking around to insure my coop. I've noticed that when I used confused.com it asked about mods but, when I used moneysupermarket.com it didn't. If you then went forward and insured through moneysupermarket.com and at some point had to make a claim, could the company contest as you haven't declaired your modifictions?

Yes, the generic form that you fill in for confused.com or moneysupermarket.com will later be surpassed by a insurance schedule from your chosen insurer, on which you would need to state any mods etc, which would affect the quoted generic price for a standard vehicle.