You don't need an engineer's second opinion, you need different builders.My contractors have excavated the pads ready for the pour, however I just checked them and they are way off the intended positioning
You're not even out the ground yet and they have messed up twice with crap advice. What does that tell you?
If you dont' build to the engineers design, then the work is invalid, won't be covered by his insurance and potentially rejected by building control.
Having said that, there is typically a lot of tolerance in pad design. The probelm you have is that there is no-one there experienced enough to know what can and can't be done. I doubt you will get such reasurance from here either, as it's not something that can be answered definitively on a forum.