mtd is a Linux driver subsystem for accessing raw NAND or NOR flash devices that don't have an SSD's Flash Translation Layer (FTL) in front of them to provide features like wear leveling. It's most commonly encountered in embedded systems.
Thank you for the education.
In some SD cards you can use proprietary magical commands to communicate with the firmware and update it or ask it to mess with the hidden sections for you, but those options aren't exposed to any disk copy tool I know of.
The performance pitfalls are not stated, but I'd guess they're referring to the possibility of using suboptimal file system block sizes or alignment. I wouldn't worry too much about recent tools getting alignment wrong or recent cards being overly sensitive to block sizes.
The official SD tool probably also ensures that it uses the exact filesystem called for by their standards (ie. when to use FAT32 and when to use exFAT), as a guarantee of compatibility with any device that interprets the standards too strictly.