Effectively the same ship except different drives, power plant, hull (engineering section, remember?), controls, and crew composition (more engineers, more support personnel).Modifying an existing design would make training and maintenance easier (it's effectively the same ship, just with longer legs).
No offense, but this sounds like a huge handwave to me. The sort of thing I might come up with if there had been a canonical statement about X-boat tenders being the only sort of ship the Scouts used other than Scout/Couriers. If your theory had any validity, how come the survey ships aren't modified tenders too? You could stuff all the survey equipment you need into a 1000T hull. Indeed, you can stuff a lot more survey equipment than you need into a 1000T hull, which seems a pretty good reason to build a dedicated class of survey ships. But the same argument applies equally to transports and any other sort of support vessel.
And, to go meta for a moment, it seems an unnessecary restriction on the game universe. If a referee want's to run a scout campaign, shouldn't he have a bigger choice of ships to give to his PCs? "I can't give you a Fat Trader, guys, the Scouts only use Scouts, Donosevs, and X-boat tenders. Oh, and AHLs..."
Hans