The Pi3 may have a quad core processor running at 1 GHz, but it is unlikely to be as fast as a desktop or server machine. There are several reasons for this: limited RAM 1GB, slower clock speed, slower disk access etc.
In short expecting similar performance between the $35 Pi and a desktop x86_64 machine is unrealistic. This is an apples to oranges comparison.
If your application is complex enough to require a dedicated architect the Pi may not be an appropriate choice from a performance perspective. The Pi can do many things but competing with a desktop on an equal footing is not one of them. if it were, given, its price point, the Pi would be replacing PC's in large numbers.