Thinset mfgs will recommend you the right primer to apply on the drywall mud , prior to the thinset.
As an example , Mapei recommends Primer L --- 1 part primer and 3 parts water ratio --- to be applied over gypsum products . Planicrete AC --- 1 part AC and 1 part water ratio --- if I remember correctly , is also recommended .
Give them a call , I am pretty sure they have a primer for your application .
P.S. We don't recommend the tiled areas to be drywall mudded , but who listens to us .