The Standard Model has not yet been cast in the language of AQFT, as far as I know. (In general, I don't think the Yang-Mills theory is put into the AQFT language yet). Therefore your question is rather vacuous at this stage. You need to ask it again later when the SM is properly formulated in (a certain extension of) AQFT.
In any case, as far as the practical calculation of physical quantities go, the final result should be independent of the formulation. For example, the canonical formalism and the path-integral formalism both give the same Feynman diagram and give the same numerical answer. The AQFT, once developed sufficiently to be able to treat the Standard Model, should give the same answer too.
So, the "new" formulation, when it becomes available, won't drastically change what physicists think. Of course a new perspective sometimes help to broaden your perspective, but that won't change the experimental prediction.
This post imported from StackExchange Physics at 2014-08-23 04:59 (UCT), posted by SE-user Yuji