Same reason a European beer tastes better in Europe, hot off the press 
I think it is the opposite I think it's because the cart has sat longer before it was vaped. Think about it the cart is filled and placed in a box and shipped, giving it time to fully saturate the whole cart while it's being moved all around.
When we fill a cartomizer I bet it is vaped within days if not hours/minutes of it being made and isn't being moved around at all. I think more time along with agitation would allow more complete saturation of the batting inside.
Sounds like the most reasonable reason.
tbh, it did take me a while to 'get' refilling. i still don't know what precisely i was doing 'wrong' in the beginning. i think a big part of it was overfilling, and being able to measure accurately with a syringe was probably the reason that worked so much better for me from the start.
if i let my cart dry completely, or use a blank cart, they taste the same. but... i fill by syringe.