Not sure if this is a bug or a feature.
When JEs are researched, one of the component is Squadron size. We start out with 3 ships. I have always taken this to mean that any JE-equipped ship can take up to 3 other non-JE-equipped ships with them when they jump. But I routinely have a JE-equipped ship escort 4, 5, or 6 ships that aren't so equipped into a system. So what does Squadron size really mean?
Also, if I have a JE rated to jump 6000 tons on a 4000 ton ship, shouldn't the 4000-ton ship be able to escort ships from 4001 - 6000 tons that have no JEs? Yet it does not work that way (or hasn't in past versions, maybe this is different in 3.2).
First off, you are correct about the squadron size, it means what you think. However, Steve differentiated between combat jumps and normal jumps so that players wouldn't have to deal with tedious shuttling back and forth during routine movements. If you look at the movement orders, you'll see a selection for "combat transit". This will limit the number of ships transiting to the jump engine's squadron size rating, and will cause the transiting ships to appear at a random location on the far side of the warp point based on the engines "jump point distance" rating.
As for the ship size rating, Aurora limits the maximum size of the escorted ship by the lower of the escorting ship's jump engine size rating and the escorting ship's size. So, if you design a 4,000 ton jump ship with a 6,000 ton jump engine, as in your example, that ship will only be able to escort a maximum size of 4,000 ton ships through the warp point. IIRC, Steve did this to prevent the construction of small jump ships.
Kurt