The parts used from unauthorized service providers are often low quality that do not compare to genuine Apple parts. This can lead to a significant change in overall performance of the device.

An imitation (non-genuine) part could cause additional problems for your device.

Deteriorating colors and dispersion of brightness in the screen.

Overheating battery or motherboard

Short-lasting battery life etc...

Some Apple devices are specifically designed to not be disassembled, making it extremely difficult (nearly impossible) to be taken apart. 
In the event that disassembly takes part, it is almost certain that there will be cosmetic damage to the device - scratches on the display and/or cracks around the edges which result in loss of resale value. 

In case of unauthorized service or third - party parts on an Apple device, even if a third-party part is used or not, the device loses the support/warranty of the provider (Apple) and a repair cannot take place at an authorized service provider - either covered by warranty or not.

Only Authorized Service Providers can offer full support to devices under warranty and out of warranty repairs, while also handling exchange programs and other repair programs that Apple announces through their official websites.