hi there
the exisiting Drupal is in example.com/website
the new WP is in example.com/blog
as far as I can manage the two programs are in completely separate subdirectories, and can’t see how Drupal should interfere with the WP sub. Although as you say its not a completely clear root folder.
I will also use separate MySQLs. (I’m not going to migrate the old DB either – starting from scratch, but need to leave the existing Drupal content live for the clients audience.)
The Drupal db was done by another programmer, site now to be replaced by WP theme.
My other option is to use completely different host to build (and then migrate to replace thte Drupal), but that will cost me.