Yeah, the entire logic breaks down as soon as you look at your own fleet in the campaign.
It's travelling as a single large blob. The ships move and maneuver at the same rate as the slowest ship so as to stay in a mutually defensive formation.
Let's justify the logic behind this and what it means.
One cannot simply go around a defending fleet with fast ships due to the geometry (the defender only has to travel a short distance to intercept the attacker, while the attacker has to pick a direction and close) and the simple fact that one can intertwine logistics ships with combat ships- think "vulnerable" aircraft carriers sitting in a single formation with their escorts- a patrol boat cannot simply go around the destroyers. Your zombie Paragons could easily slot into the same line as a bunch of Atlases- they move at around the same speed. Suddenly the clever ambush would run into a convoy line that has 2 Paragons per logistics ship- seems to be the average ration of warships to logistics ships. Think WWII convoys, but reversed.
Even if the ships were forced to be spaced, there is no reason for the ships to be arrayed in a single file line. All indications show that the ships are placed in an exceedingly messy circle formation, and logic would dictate the logistics ships and slow capital ships be placed in the center.
Besides which, what would the spacing even be in Starsector? The largest ships seem to be running with 1/6 the size of a modern aircraft carrier's crew complement. We'll assume extensive computer support, especially in the high-tech ships- I'd say at the very maximum 2 kilometers long. Probably more like a kilometer however, these ships are three-dimensional and would certainly mass significantly more than our aircraft carrier example. Perhaps 2-5 kilometers of spacing while burning, and that gives them a significant safety margin. Cap ships can cover their own length in seconds- these ships would already be in the battlespace, and in the way of any ambitious pirates.
When ships enter pursuit mode, the ships have more like 200-300 meters of spacing, certainly a close enough formation to cover each other. Since pursuit actions mean that the running fleet has been caught- these battles normally involve the combat ships turning around and trying to punch the attackers hard enough in the nose to let the logistics ships retreat. The formation that they enter the battlespace in is the formation they were running in- no time to slow down and close the formation up, meaning that this spacing is more likely.
The idea of logistics ships sitting undefended because the fleet was in a line formation in space is laughable.
Fleets are most often detected a good portion of a day out, and it can easily be told if the fleets are coming at you or not. There are hours for the defending fleet to close up or intercept. These fleets are also detected in the stellar scale- When spotted, even single ships will be most likely a good portion of a light-minute away, allowing ships spaced only kilometers away to close up.
A frigate under sustained burn runs at the same speed as a destroyer (with abilities), 2 above a cruiser, 4 above a capital. It's faster. It also has to close a distance multiple factors larger. It won't get there.
Your best bet of pulling off an actual ambush is to wait for the fleet to get busy engaging someone else, then stabbing the logistics. If said second fleet is unavailable, the best conceivable way would be dashing out from some form of concealment, most likely just plain trickery, and defeating part of the enemy escort in detail, subsequently ramming as many missiles and fast frigates down the gap as you can. This could be pulled off by large numbers of missile frigates- the frigate's purpose is to be a strike weapon. The most logical role for a light and fast ship in a large fleet action is to screen for larger vessels with staying power and take opportunistic kills with missile weapons- interdiction and harassment. This can be seen in modern doctrine- we favor strike ships with powerful weapons, and when we build larger ships, (air carriers) they tend to be an extension of that doctrine, simply projecting more of that strike capability further.