The thing is, you're assuming a homebrewed effect to justify the lower level. Yes, there exists a homebrewed effect that does what you're describing, but there's no evidence that it was used on this occasion.
And people have been gaining stats/levels "without anyone noticing" for a while. There was no pomp and circumstance when V revealed
Power Word Stun: Until that time we still believed they were level 14.
Also also, the extra int and level can be explained hand in hand: Upon reaching level 16 (and any multiple of 4), you can raise one of your ability scores by one. So going from Level 15/Int 23 to Level 16/Int 24 is perfectly acceptable.