Update variationReference.avdl

We've clarified some language and asked some questions where we are unsure.
Recently there were several discussions on the VCF spec mailing list about Phred scaled vs plain probabilities. The questions were: 1) is it a good practice to have some probabilities in Phred scaled units and others unscaled? 2) is `float` sufficient or should also `double` be supported?
It was proposed there that the GP field uses plain probabilities in future versions of VCF
https://github.com/samtools/hts-specs/wiki/Proposed-updates-to-VCF-and-BCF-specification

Personally, I like best phred scaled or log scaled likelihoods because even extreme values can be represented with floats.