No, the american version isn't stretched, but I think you can fix the e version with some ini editing, but I don't know how. As I remember somebody posted what you have to do.
Check the 1964 board too. Under PJ64, the ini file now uses the extension "rdb". Edit the rdb file, and under the appropriate entry for your euro rom add this line:
Resolution Height=240
In order to propagate this fix to 1964, copy the PJ64 rdb file to the 1964 folder. If you use Jabo's D3D plugin (who doesn't?) that's it.