Update variationReference.avdl

We've clarified some language and asked some questions where we are unsure.
This isn't specific to this PR, but what's the benefit of using a GADNASequence instead of a String? I ask because we explored this in the ADAM project and found that it was nominally easier to use strings. The main advantage that we found to using an enum was the ability to enforce alphabets (e.g., a DNA base is one of A, C, T, G, + IUPAC codes), however, we came to the consensus that it would be preferable to enforce this via run-time checks/asserts. Strings were easier to use because they're supported as first class citizens of most programming languages, which makes pattern matching, comparison, etc. simpler. Additionally, we didn't see a great performance improvement (in both data structure size or raw performance) from using enums.