No, that move will still be possible and is (effectively) unchanged.
The dive-under is to allow trains to depart Acton Yard towards the Reading direction without conflicting with Up Relief Line services towards Paddington / Crossrail, which are sent via the dive-under.
Up Relief passenger services will, I believe, still have an option of taking the 'flat' route when there is no conflicting freight service, as this will be very slightly faster than dropping via the dive-under.
The physical arrangement of the flyover also happens to mean that freights into the yard from the Reading direction will also 'fly over' the Up Relief dive under, but in operational terms this is no different to today.