Update variationReference.avdl

We've clarified some language and asked some questions where we are unsure.
@cassiedoll OK, gotcha. This is possibly divergent, but are the IDs supposed to be universal, or do we allow IDs for alleles to vary between vendor? I can understand the underlying, vendor-internal ID being vendor specific, but I think it'd be very difficult to use the API if vendors return inconsistent site/allele IDs.