Yes, such issues can be very troubling and defects can be more than meets the eye. Its true that the ID can conver up certain defects but there are others that are harder to compensate for. Your ID might even charge you more for the additional touch up work.
As as first time homeowner its understandable to have doubts if you are actually nitpicking or not. One should keep in mind that its normal for defects to be found, as there is no perfect construction even for a new home. If you wish to seek a second opinion, you might consider engaging defects inspections specialists to assess if the defects are superficial that could be let go or there could be others that needs to be addressed before you start your renovation.