I'm just getting started with eShop, but here is what I plan on doing. I'm in the US, so USA addresses are zone 1. Canada is zone 2. Those Class A rates will be for First Class. Did you know you can add some text under that shipping table? Just go to "Pages" - Shipping - Edit. Leave the little table code alone for now, and just add some explanatory information below it. For example, here's what mine will say: (when they click the shipping link from checkout pages).
First Class Shipping to any U.S. address is free.
Free. Period. No minimum order. No matter how many items your order!
At this time, we only ship to the USA and Canada.
Shipping to Canada is a flat rate of $5.
Please see the product list if you wish to add Priority or Overnight Shipping. You would add these to your cart as an additional item.
Then I will just make a "product" for Priority Shipping (add... oh say $6. or so) and maybe $20 for "Overnight." I can do this because my products are all small and lightweight. I may lose a little money on some shipments, but I might make a few cents here and there. I figure, overall, it all evens out. And the customer knows I am not gouging them on shipping. Everyone hates that.
I may go into the code and add some text to that table, but it may not be necessary. You could also just remove the short code for the table from that page and just write your own explanations. You can make that page accessible elsewhere too, like on the sidebar, via a text widget.
Anyway, just thought my approach might give you some ideas for a workaround that will meet your needs!