As you found out;
Portable does not install anything into your system configuration. You will need to do that step (add filetype to the Open With list) yourself.

Was there a reason to go to 'Portable' (which is a 32 bit version)?
You CAN use installed Calibre with a Library that is part of 'Portable' (on a removable drive). Just lock the drive letter on the removable drive (I use L:

)