EBay never could combine invoices that were in different currencies, so that's one possiblity.
And there is no compatibility between the dotCOM cart and the dotCA cart.
Your best bet is the Paypal invoice system you have already discovered.
However, you might consider adjusting the combined shipping charge, which can include "handling" charges, to allow for the eBay fees on the uncombined postage.
And no, it's not fair.