Are Chelan Beauty apples GMO? 

Chelan Beauty Apples are not GMO. You cannot have a certified organic variety if it was genetically modified. All certified organic apples come from non-gmo rootstalk, scion or bud wood.

How are "specialty varieties" created if not GMO?

SweeTango apples are a great example of a hybrid apple, not a GMO. It is a cross between a Zestar and a Honeycrisp. This cross occurs through cross pollination with bees and does NOT involve any changes to the genetic makeup of apples, trees, or seeds.  When universities create new varieties of apples, they do this through scientific breeding programs which are as natural as breeding programs involving animals.  Here is an article about the SweeTango apple that goes into further detail:

Does Chelan Beauty "own the rights" to grow apples like SweeTangos?

The way the ownership rights work with this particular variety is actually to the benefit of small high-quality farmers. The patent is protects the integrity of the name SweeTango so that large corporations can't flood the market with poor quality SweeTango's. Here is a good article about it.