The confusion is understandable, as the history is messy.
At one point in the past English had both (as Icelandic does
now), but subsequently edh disappeared and thorn was used for
both voiced and voiceless forms. Since early print sets didn't
have thorns, people did another substitution, using "y" for thorn, as the two letters are somewhat similiar in shape and don't conflict much (few minimal pairs). Thus we get "ye olde tea shoppe" -- and of course, even later on, people read that with a "y" rather than a thorn and get even more confused.
<pedantry starts>
It all starts with speakers of one of the ancestral Germanic languages using a varient of the alphabet in Northern Italy well before the Roman Era. They wrote on wood or scratched on stone, and changed the letter forms to suit the material: lots of verticals, no curves, horizontals become diagonals, etc. This leads to the many runic alphabets. But the bottom line is "D" becomes thorn, which is nicely ironic.
When English begins to be written in the Latin alphabet, thorn and another letter (used for some kind of spirant and later on replaced by "g" or "gh") are borrowed to represent sounds in English not well represented in the Latin alphabet. They are gradually replaced by Latin letters.
I don't know the history of "edh", sorry.
<end of digression>
Dragging this back to Wolfe by main force, I note that we have evidence that Severian's alphabet is like ours: at one point we are told that "s" looks like a snake and "t" like a cross. Are there any other hints?
-John Bishop, letting his long-ago linguistics degree
take over for a minute or two.