I hate to say it, but that was a schoolboy error handing the car over (irrespective of its condition) without an agreed value, including any mods, from the insurer.
I've always been screwed over by the insurance company when they've had the car before I got any money. Cheapest raggedy old dog was always the 'market value'.*
Last time I had my vehicle smashed I had it recovered myself and the insurance company were told they were allowed to inspect the vehicle but under no circumstances were they to take possession of it until I had decided on what to do with it and we had haggled out an agreed value - ie them offering me a bs cheapo value and me countering with the actual value of the vehicle given age/mileage/condition/servicing and new parts etc.
Granted yours is a newer vehicle, so I hope you get a decent payout for it.
* I had a motor written of as uneconomical to repair - it needed a new wing, a headlight and a bonnet; vehicle was taken away to the insurance companies storage site. 8 months later I get a fine from the DVLA because my vehicle was seen being used on a public road without valid road tax. I think my vehicle was sold off, repaired then used by someone, possibly the garage it was kept at. Who knows. Terrible service from the insurance company either way.