Even when you look at the high end of the "player sized" ships, 2000 tons, it's still arbitrary. If you take the lowest jump 1 drive for a 2k ton ship, you get the K jump drive and it's 55 tons.
Now if you hop over to High Guard and start designing a 3k ton ship, to get it a jump 1 drive you take the tonnage (3k) and multiply that by 2% to get the jump drive tonnage. That's 60 tons. So, to move a ship that is 50% bigger, it only takes five more tons of jump drive?
If you even want to get really nitpicky you could go for a 2001 ton ship. For a jump 1 drive on that ship it would be 2% of 2001, so 40 tons. That's fifteen tons less than what's required for a ship that's 1 ton smaller!
Now I get the point that on 100-2000 tons ships that off the shelf drives makes sense, hence the A-Z drives. I have no problem with that. For ease of use it even seems that it's fairly linear and simple on the table on 108. I'd have liked to see a formula so that odd sized ships (150 ton or 1500 tons for example) were better represented, but I can extrapolate that information easily enough on the off chance that my players want to build one of those.
I was just confused as to why 2000 tons was the oddly arbitrary drop off point for suddenly much more efficient drives. It would make more sense that as you went up in size it wasn't so linear and the drives became more efficient at moving larger ships. Then you hit the 2000 ton point the size of the drives was inline with the next step up in the High Guard book. If the simple answer is "tradition", that they were following classic traveller as an example, it's disappointing but understandable I guess. I just wish they would have fixed the glaring discrepancies in the old system while updating.

I never played classic traveller, it being a bit before my time. I only megatraveller, and the one after that...New Era? Never cared for the whole Virus idea. I seem to recall the book for creating ships back then requiring a huge amount of math, and probably took just as long making deckplans...