They had added an optional rule that allows for a ten card sideboard and the wishes can get cards from it. Since the exile zone is still an in-game zone it is prohibited as a wish target but getting it from the sideboard is fine.
Taken from
these rules:
Optional rules for EDH
1. EDH Sideboards
Rather than filling every deck with banal responses, it is preferable to allow some flexibility in the composition of a deck.
* Players may bring a 10 card sideboard in addition to their 99 cards and 1 General.
* After generals are announced, players have 3 minutes to make 1-for-1 substitutions to their deck.
* Any cards not played as part of the deck may be retrieved by "wishes".
Reasoning:
Highly tuned threats piloted by skilled opponents mandate efficient answers. The minimum number of response cards required to ensure they are available in the early turns can easily overwhelm the majority of an EDH deck's building space.
Sideboards allow players to respond to the "best" strategies in a timely fashion . They should be strongly considered as a necessary defense against brokenness and degeneracy in an EDH environment where no gentlemans agreement on style of play exists.
