When you send a VC Pokemon through Transporter, its old IVs are ignored for all purposes except gender/shiny/Unown shape, and replaced with a new set that uses the modern structure (so 6 independently controlled stats instead of just 4, and each one has twice the precision) and a guarantee that at least three of those stats will be maxed out. The IVs it has after transfer bear no relation to what it might have had before, and this is not an inconsistency (at least not for a static encounter like Mewtwo).