I guess that'd really depend on who was involved in the assessment of the cars damage; the insurance company may well outsource it to the garage which are doing the work, they may not be bothered about the mods as they will want the money for the repairs.

The problem you've got is if you have made these mods and crash into other people, perhaps taking down a bridge as you go! The insurance company won't be wanting to pay out tens of thousands if they can help it - and that clause in your contract with them, can get them out of it. At the end of the day is it worth the risk?