I’m having trouble understanding what BEP-47 exactly is. Care to enlighten me?
Using padding files to prevent torrents containing multiple files from getting stuck at 99%.
The original Bittorent spec has a really stupid design decision in that it is just a long stream of concatenated files split into fixed size pieces. This means you always have to download parts of adjacent files to get the file you actually want. This leads to all sorts of unnecessary complexity when partially downloading a torrent of what do this with this left-over data, eg qB saves hidden ".<sha1>.parts" per torrent, which you can easily lose.
To get around this, padding files where introduced that "fill" the gap from the end of one file to the start of the next piece boundary where the next file starts with 0x00 filled padding files with naming corresponding to length. It's a cross-client standard defined in BEP47. Padding files are also required by necessity for hybrid Bittorrent v1+v2 torrents. Any remotely decent torrent client won't transfer or save these padding files, so the size doesn't really matter. And even if your client doesn't, some of the padding names will likely overlap and only be saved once.
If you don't understand, then just think of it as the solution of 99% stuck torrents and need to download part of other files' pieces to check if given file is valid.
These files are the cause of torrents that are stuck at 99%
Quote from your link: "If used incorrectly or maliciously symlinks and padding files can result in internally inconsistent torrents which cannot finish downloading because they contain conflicting hash information."