This was the limitation of vision that LBB2 suffered from, which LBB5 liberated us from.
Also, you can't have LBB S9 Fighting Ships without LBB5, so ... yeah.
I was apparently not being clear.
If in a situation where I only want to use Book 2 designs (likely because I am intentionally only using The Traveller Book and a couple extra items), then I still use the Book 5 pp fuel usage. When limiting myself to Book 2 designs, MTU still includes large ships, they just don't matter as they are outside the scope of what PCs get to directly deal with. Again, in this scenario I am intentionally limiting myself to The Traveller Book and things directly compatible with it. Note that in this situation, the usability of Supplement 9 is utterly irrelevant, as none of those ships are PC usable. The idea of limiting oneself in such a way might be alien to you, but it is useful and I will do it when it makes sense to me.
In a situation where I have completely opened things up, then I will only use Book 5 designs, and will mandate that all Book 2 designs have to be rebuilt using Book 5 rules, no exceptions. Interestingly, in this case Supplement 9 ships are only of marginal usability, as they don't really follow Book 5 rules, anyway. You pretty much have to remake all of them, too. (In fairness, I can only do all of this because I still have a copy of AMV's High Guard Shipyard laying around and it still works on Windows 10.)
As far as "liberating" from Book 2 designs, the one thing I would note about Book 2 designs is that they are still useful to keep in mind, as they give a good idea of the limitations that you would see in civilian designs. The fewer turrets, the complete lack of armor, the limited weapons (only lasers, missiles, sand) are all good guidelines for what civilian, even armed civilian, ships should be limited to. If, however, you are looking for military designs, then, yes, Book 5 is to where you should turn.