This is true. I just don't want to build 5001 ton destroyers. But a way to potentially balance it would be took look at the cut-offs holistically. If the same breakpoint gives a bonus and a penalty, then the 'advantage' of wonky 4999 and 5001 destroyer classes will decrease.
So, giving it a little more thought. Each breakpoint should have a pros and cons chart (and they should be 'round' numbers and match so it wouldn't be a case of one entry saying 'less than than' and another saying 'more than' leaving a sliver of confusion). So target size, bridge size, crew size, feature size, armour /hull point mods, should all line up: 5000+ gets you this, 25000+ gets you this, 200+ gets you this, etc.)