[wtallis]

I don't think the page actually says that the security section has anything to do with the potential for poor performance; those are discussed in separate paragraphs. It's mentioning the security section to warn the user that this tool will not actually wipe every byte of the card, just the normal unsecured data storage area.

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.