You're right about a dedicated person (not necessarily a Muslim) having a different understanding of the Quran than an average one. But that "different" doesn't mean contradictory or something totally unrelated.
The way I see it, the difference is in the depth and perspective of the meaning. Every verse in the Quran has an easy meaning, that is the literal meaning of the sentence/verse when read in plain Arabic. But then there's also the deeper (or hidden if you like) meaning that arises from the way the words have been used. Arabic language is very rich in terms of conveying different meanings by the way words are put together. I will give you an example:
These two verses are from Surah Ash-Sharh:
Which mean, respectively:
For indeed, with hardship [will be] ease.
Indeed, with hardship [will be] ease.
Once a scholar explained that the word 'hardship' (Al-'Usr) has the two letters A (elf) and L (lam) in it, which in Arabic it is used for definitive reasons; meaning, the two words in the verses both refer to the same 'hardship' that is being talked about. Whereas the word 'ease' (Yusr) is without A and L; and this is because when used without the two definitive letters, they mean two different things. So, he said, from these verses, we can understand that for a single 'hardship' there is more than one 'ease'.
This is just an example to show what I mean. Qur'an is full of these examples. Also, the Qur'an is not for a certain age in time, it's for all the time from the day it was revealed to the day this universe will come to an end. Because of that, the verses may be interpreted in different ways in different times in history. This is because humans develop and learn/understand new things. Those new ideas and developments bring along new comprehension to the Qur'an. It's more like, when you just learn a new concept and later you realize that it was actually mentioned in the Qur'an, you go "Oh right, THAT's what that verse must have meant!".