Having just had to take apart my top box lock in order to ascertain why a newly cut key (Ilco x132) was not working, I can confirm that the GiVi-manufactured top box does use a GiVi-type wafer lock cylinder. I would venture to guess that the OEM pannier locks are also wafer-type (rather than pin-type), and they do work with the OEM ignition key, but the difference is the keyways in the lock cylinders are different. If the Honda key actually fit into the GiVi lock, it could probably be made to work (given access to enough different wafers to swap to match the ignition key profile). However, my Honda key certainly does not fit into the GiVi cylinder, and it is probably not possible to swap the pannier-type cylinders into the top box.
Ciao,
[EDIT: Forgot to mention that I got the ILCO X132 key working--the outside grooves needed to be widened (such that they were no longer "grooves"), as this was preventing the key from inserting fully.]