Well, yeah ... first few levels should come really fast.
True, if you skip final Nautiloid fight, and just connect the transponder, you loose some sweet XP boost ... but you can get it pretty fast elsewhere.

So, i would gues that this is intented.

In the words of the senior NCO instructor at cadet battalion:
“If you ain’t cheating you ain’t trying. And if you got caught you didn’t try hard enough!”