Why are these two same rated metallized film capacitor physically different
I wouldn't worry.  Their measurement is the same, and their rated maximum voltage is the same, so it should be a drop-in replacement.  There are a number of reasons why they might be different physical sizes.  For example, they might not have the exact same materials (maybe one has a better dielectric, or the metal film layers in one are thinner).  They could also have different geometry internally, there's no reason the layers need to be perfectly flat.