Each ship does indeed have its own boost profile, from how much boost it provides to how frequently it can be used and how much additional speed (and flight profile gains) it gives.
If you want a game-canonical reason, let's simply say that some ships have stronger engines and can therefore boost more often.
As others have said, maybe there's confusion on what the pips actually do. It only APPEARS to you that you have to wait til all 4 energy bars are restored. You don't, you always have to wait the same amount of time (for that particular ship), until you can boost again. You can verify this for yourself by setting eng pips to 0, then boosting. You will note that you do not recover any energy bars at all, yet on the same time interval you will be able to boost again, as long as you still have 4 bars left in the cap. When you do not, no boost for you.