What is the difference between formatting sd card via pc and phone? Almost every question about problem with sd card have answer "format sd card by your phone". So what is the difference when I format sd card by PC or by phone? (file system is fat32)
None really.

I suppose the biggest reason why people make such recommendation is because an end user could easily end up formatting the card with an incompatible filesystem, like NTFS.

This in turn will cause further confusion to the user and additional forum posts. 

It is safer to just ask them to format the card using the phone's interface.