Interesting! For my first order I printed one ship plus 3 sets of Dauntless batteries (back in the day, I bought 3 mispacked blisters without batteries and they've been languishing to this day 
) and I put them all on a sprue to avoid multiple handling charges. You're saying it's fine even without the sprue as long as it's in one file? I guess I wasted a bit of money on sprue volume then, huh.
It can vary, although the 5$ charge is a flat rate, at the same time if you submit a file with 50 small parts don't be surprised if it gets rejected because it results in such a large amount of time to process those 50 parts even though it is still technically "one file".
I try to sprue up as much as I can without it being without it being too obnoxious and I aim to not have "single" parts floating around, when I was doing my
Grey Knight Gladius I had few enough parts per ship that I could make
each ship it's own sprue and didn't try to connect each ship together either.
It's got a bit of a learning curve to it! I've been using Shapeways for about a year and a half now but that was mostly in Strong and Flexible and these
Grey Knight ships are my first serious use of FUD.
