Page 19 of that document - Flat Rate Quick Reference says....
Note: Flat Rate prices are available when material is sent in a USPS-produced Flat Rate Envelope or Box. When sealing a Flat Rate Box or Flat Rate Envelope, the container flaps must be able to close within the normal folds.
Tape may be applied to the flaps and seams to reinforce the container; provided the design of the container is not
enlarged by opening the sides and the container is not reconstructed in any way.