When cost is evidently the single most important metric we're being judged by, throwing in options which do not enhance the ability to do the one thing the ship needs to do seems kind of risky. The purpose of this ship is to ensure that civilians cannot literally outrun the law. Everything else is secondary, and might draw questions from the procurement board.
You don't even need to escort it. The entire purpose of this project is to build a ship that can chase down unruly merchants and smugglers trying to escape the system. The ship with contraband can spend an hour or two flying back to a station to have the contraband processed, or we can call in other assets as the Denubian design intends.
I don't think the cargo bay is terrible. It'll allow the protector to be completely superior to the Tellarite design at an increased cost, which might be compelling. But an in-system inspection ship has so many options to deal with cargo that I don't think it's a major improvement, and the last update repeatedly implies that we should try to cut out as much as possible.
What the tractor beam, the brig and the cargo hold really let us do is to stop the ship, the crew or the cargo respectively. If you can hold the ship you don't really need to hold the other two, as the Denubians have designed for. But the crew can still present a risk to you, their ship, or their cargo, so having a brig to separate the crew from the ship and the cargo will be useful.
So then is there any scenario where we want to be able to separate the cargo from the ship and the crew? The one being presented is where someone has contraband that we want to confiscate, but how often are we going to want to confiscate some small amount of contraband without destroying it and then let the crew and ship leave the system? Shouldn't we at least try to interview everyone on board a ship that's been caught smuggling?
