Well you're splitting by size, a system defense boat can be any size...

Actually, I realized this is based on certain assumptions. Traveller assumes that a hyperdrive is big, expensive, & fuel hungry. Things like StarWars hyperdrives are cheap little things that are mostly generic & compatable with most ships. Even their little A-Wing fighters have cross-galaxy hyperdrives and fuel enough to get pretty much anywhere.

So if you're using big & expensive hyperdrives and a nation doesn't want to come across as an interstellar aggressor it builds system defense boats that are cheaper & better in whatever weight class. Hyperdrive warships capable of extended missions become pure "intent to invade". Another effect of this (may not apply in your setting depending on hyperspace travel details) was the creation of jump frames. Just a huge jump drive, fuel tanks, and an open framework. If you had bunches of system defense boats that needed moving (or you wanted to attack someone without building jump capable warships) you built the jump frame and maybe a couple support boats, clamped everyone to the frame, and the whole thing went as one ship.

There are trade-offs of course. With a fleet of hyperdrive warships you have operational flexability & resilience. With specalized boats & a jump frame you have better per-boat performance but you have to move them as a group and tactics change because loss of the jump frame matters.

Again, it depends on the size & cost of hyperdrives. It also only makes a big difference at the economic & geopolitical levels, basically just setting background for most games. Most PC groups in these games never go past one heavily armed trade ship. The biggest difference will likely be if local law enforcement is seriously combat better at equal sizes of ship but can't chase the PCs into other systems or if they're somewhere around equal to PCs at equal ship size but can chase them out-system.