Exactly, the difference boils down to: (a) is the calculation itself the end goal--e.g. am I trying to draw a plot which shows the motions of the three bodies?

Exactly, the difference boils down to: (a) is the calculation itself the end goal--e.g. am I trying to draw a plot which shows the motions of the three bodies? or (b) am I trying to use the code which describes the motion of the 3 bodies as a modular part of a system to answer other questions, perhaps interactively. If everything is a one-off, and you're working on a very small team, of course excessive abstractions make little sense. But that's not how engineering is done. Abstractions are really important, because they allow us to collaborate.