When a sunroof is installed from the aftermarket, it breaches the structural integrity of the vehicle. The roof comes as an integral part of the car's overall frame. It bears the structural load as well. Whenever the roof is cut to install a sunroof, it affects the rigidity of the roof and makes the car's frame vulnerable in case of a major crash. The automakers perform extensive research to ensure the sunroof doesn't compromise the car's structural integrity. However, in the case of aftermarket sunroof installation, there is no such thing.

Sunroofs installed in cars by auto manufacturers are supposed to go throughout the life of the vehicle. Many aftermarket sunroof manufacturers claim that their products are as good as those made and installed by the OEMs, however, this isn't the case here. A car's sunroof system comprises a host of mechanical components. It has a lot of moving parts, which adds to the vehicle's overall weight. These mechanical parts of aftermarket sunroof systems often start malfunctioning and eventually stop working in several cases. In such a case, it becomes a costly affair for the owner to fix it.

Due to unequal or ill-fitting seals, aftermarket sunroofs are often prone to water leakage. Water can cause damage to the sunroof's motor mechanism, which can be an expensive affair for the owner to repair. The components of sunroof systems are often damaged due to the water leak. In addition, adding a sunroof to the roof implies adding extra seals, which eventually results in an increased noise level in the cabin.

Many automobile dealers and individual car buyers don't want a car with safety issues. Small tweaks and installation of aftermarket features that don't impact the structural integrity are not a problem, but the installation of an aftermarket sunroof impacts the vehicle's overall frame significantly, which results in many buyers shying away from buying the vehicle. Therefore aftermarket sunroofs have a huge impact on the resale value of a car.