Instead of the often shown flying jeep, it's size suggests that is more a sort of flying light truck/forklift that most traders carry to assist with loading and unloading of cargo and passengers.
This is my interpretation as well.
When you're playing "new design buyer" you look at the tonnage allocation for vehicles and often think of it as dead weight/wasted tonnage. The 4 tons spent on an air/raft
could have been used for another (high passenger) stateroom or +4 tons of cargo hold capacity, both of which can generate revenue when used (unlike a vehicle berth). So from a min/max perspective, vehicles are a "loss" for the bottom line of mercantile profitability.
Flip that around into playing "end user operator" and the perspective changes. Having berths for your own vehicle(s) onboard your starship makes it possible to operate in locations other than a starport. If you don't have the infrastructure of a starport to assist with the loading/unloading of passengers, cargo and freight ... because you're doing that somewhere with limited infrastructure support ... you're going to need to "bring your own" means of mechanized assistance (otherwise, you're doing everything "by hand" so to speak). In this regard, having an air/raft is VERY HELPFUL for the marshaling of cargoes during loading and unloading.
Are there "rules" to this effect?

No ... there aren't.
Does this kind of conclusion become obvious when you think about it for even a minute (or few)?

Yes ... yes it does.
Vehicle berths are what make a starship "expeditionary" to austere locations, away from starports. Without an organic vehicle support component to assist with the marshaling of passengers and cargoes, starships become entirely dependent upon starport infrastructure just to be able to organize the loading and unloading of those same passengers and cargoes. Kind of like how airplanes which don't have fold down doors with steps built into the fuselage will need ground services at an airport to provide a way for passengers to embark/disembark along with services to load/unload the cargo hold of an aircraft. Whether that's a gate tunnel or a ladder cart (for passengers) or a conveyor belt ramp and cargo/luggage carts, those ground support services are provided by the infrastructure of the airport.
Now think in terms of a Boeing 737 or Airbus 320 NEO (or whatever) needing to make an emergency landing (on the ground) ... somewhere ... other than an airport. A place where there is NO ground infrastructure to simplify and speed up loading and unloading.
How do the passengers and crew exit the aircraft?
Emergency inflatable ramps (that are designed to be used one way), clambering down off the wings (again, intentionally one way) and maybe ... maybe ... a fold down stairway at the aft of the aircraft (which might be used for two way access).
How is the cargo extracted from the cargo hold?
Short answer, without mechanical assistance ... SLOWLY AND PAINFULLY ... by hand. Depending on how the cargo hold is "packed" (and with what) this could be potentially dangerous (especially if the cargo "shifted" at any point). Most commercial passenger aircraft do not carry a (skilled) supercargo crew member onboard, since all of the cargo operation skills are "outsourced" to ground crews at airports (part of the airport infrastructure) rather than being organic to the cabin crew. The basic idea is that a supercargo "skilled" member of a ground crew can service a LOT of planes in a day, while a supercargo "skilled" member of a cabin crew can only service 1 plane at a time ... so in terms of skilled crew utilization, it makes a lot more sense to "outsource" that skill from the cabin crew to the ground crew(s) at airports. It creates a dependency on those ground crews and their associated airport infrastructure, but in commercial passenger airline services that are only doing point to point travel between airports, that's not a detriment to operational organization.
As soon as you switch over to more of a "bush pilot" type operation, where airplanes are flying in and out of austere locations with little to no supporting infrastructure ... being able to load/unload your aircraft "by yourself" without ground support infrastructure takes on a whole new meaning. Think of a seaplane that pulls up to a jetty onto water for loading/unloading (the equivalent of a type E starport, in starship terms). If there isn't even a jetty onto the water for a seaplane to pull up to, you're looking at the equivalent of a type X starport (in starship terms) for loading/unloading.
To broaden the analogy back out to the starship operator end user experience, having an air/raft on board ... in effect, allows you to bring some minimal amount of ground support infrastructure services "wherever you go" with your starship. An air/raft is "environmentally agnostic" (gravity, atmospheric composition usually aren't issues) in operation and can be used as a "sky crane" for lifting loads that would be inconvenient/hazardous to do by hand. An air/raft can be used to ferry passengers (and crew) to/fro outside the starship without having to "worry" about walking or elevation/access issues. So there are a LOT of "local logistics challenges" that an air/raft can "trivialize" when a starship is "parked" at an austere location (away from starport infrastructure).
From a Traveller gameplay perspective (Player and Referee), an air/raft (or equivalent) could be almost invaluable as part of a smuggling operation. You don't need to take the starship proper to a smuggling exchange, only the air/raft (particularly in the "Small Package Trade" business when smuggling less than 1 ton). The use of an air/raft reduces risk to the starship crew and is better for "on the down low" exchanges of goods, due to the smaller signature of the air/raft (relative to that of a starship). For larger cargoes/passenger transfers, an air/raft can provide a variety of support services and options that otherwise wouldn't be available/practical due to marshaling and logistics concerns.
So while from a purely min/max "revenue tonnage" perspective, a vehicle like an air/raft is just "wasted tonnage" on an interstellar merchant starship that ONLY goes to starports (go figure, eh?

) ... as soon as an operator wants to "pick up and deliver" to more locations than JUST type A-D starports (where local vehicle rentals usually aren't a problem), that is when "bringing your own air/raft WITH you" everywhere you go starts looking like an attractive option.
Therefore, if it helps ... think of having an air/raft berth on a starship as a sign that such a starship is (intentionally) designed to be operated in a "bush pilot" fashion, where starports aren't the ONLY possible destination(s).
- Type-S Scout/Courier ... has an air/raft berth standard. Pretty explicitly intended for "austere" operations.
- Type-A2 Far Trader ... has an air/raft berth standard. Very likely intended to be "still serviceable" when deployed to "austere" locations.