Update variationReference.avdl

We've clarified some language and asked some questions where we are unsure.
A meta-comment (as ID as string wasn't introduced in this PR), but it might make sense to make the alleleID a long, instead of a string. This may be preferable, depending on how alleleID is being used (e.g., as a mapping to an RSID, or to a graph node); please disregard this comment if I've missed a previous discussion RE: long vs. string for variant IDs.