If the book being looked up has no isbn, then the plugin does a title/author search and at that point that is the one single scenario at which it could attempt to choose a particular format over another (presuming that it comes back in the results). However this approach would only work if (1) the book has no isbn prior to metadata lookup, (2) the edition you want comes back in the search results, and (3) that isbn is in the same isbn pool as any other metadata plugins enabled. Which is just too small a subset of circumstances for general users to rely upon it.
To be honest I haven't really noticed an issue with the existing behaviour - the covers I get back generally tend to be around 600px high or so. Though in the few circumstances where they are not I haven't gone looking to see if there is another edition on B&N that would have given a better cover.