Why does RATT create a directory with chromosome sequences and how can I stop it?
RATT seems to be a very simple wrapper script that unfortunately does not clean up its temporary files properly. Short of modifying the code yourself, your only option is to perform the cleanup manually after running RATT.

The temporary copies are made because (a) the query is not an exact copy: RATT performs some cleaning. And (b) it needs to extract a FASTA file from the EMBL input for use in downstream tools.

The “mysterious” number behind the file names is simply the process ID of the RATT process. This is appended to make these intermediate files more or less unique (presumably to prevent overwriting existing files).