Hull Selection
Unless you have some specific design constraint (say, cylindrical ships plug into standard space docks the best), commercial shippers are going to go with the most cost effective hull design. And that is “CLOSE”. Cargo freighters don’t need to maneuver in the atmosphere. They just need to be able to land at places that don’t have high ports. They aren’t going to skim fuel because that is super cost inefficient. It is dangerous, it takes time, and it tends to put your ship nowhere near the port. Which increases piracy risk and time in the system as you have to travel to the port in normal space.
Close hulls are able to land on planets and are less expensive than “standard” hulls. Merchant ships aren’t going to be armored, so the downside of close hulls isn’t a factor. They aren't that popular in ship design because PCs need to do crazy stuff in atmosphere as part of their adventures. But I think they'd be a lot more popular in non adventurer themed ships.
Power
A commercial ship does not want to pay for more power than it needs. It’ll have enough to run its ship’s systems + its maneuver drive at the same time. It’ll turn off the maneuver drive during jump drive engagement. If the jump drive rating is higher than the maneuver drive rating, then if it is a cargo ship, it’ll use “jump dimming” and get the extra power from running the ship’s systems on minimum during jump. For passenger liners, it depends on whether you think the ship’s paying passengers will tolerate jump dimming or consider it a relic of a low tech past. Power for any weapons the ship has will definitely come from dimming the main power.
If you think your passengers would be pissed off about dimming, you might just use batteries for that temporary boost of power. They are quite cost effective compared to a larger engine that may result in more crew being needed.