I think package authors are already aware that all prefixes will be replaced. It's just that there don't seem to be good alternatives for dealing with these sorts of namespace issues as all the options have downsides.

I already mentioned what I wrote below but I forgot to reply all and also may not have been particularly clear anyway so I'll try again.

My preferred solution would be to make a special character cause the whole symbol to be matched instead of just the prefix. # is already not readable at the start of a symbol so it seems like that wouldn't cause conflicts. For example:

;; read-symbol-shorthands: (
;; ("mvlp-" . "my-very-long-prefix-")
;; ("#db" . "cl-destructuring-bind"))

The idea is that "db" is only replaced when it matches the entire symbol due to the #. "mvlp-" on the other hand is replaced whenever it occurs as the prefix of a symbol.