AVR Freaks

Yes but I think that Arduino Library hides all the complexity and the internal working of the microcontroller and so I won't be able to go deep into them. 

But this is just why Arduino was created.

It enables the beginners to start play with mproc without studying 700 pages of the datasheet. 

Evryone has some limit how deep to go.

There is a large group of people who need to create a simple program time from time. They use the functions and do not care what is inside them.

Then there are students like you who want to know the details in a function.

Nothing prevents them to find it, as the functions source code is available.

But for a scientist even a simple instruction like "LDI R16, 1" hides the complexity of what exactly happens in the guts of a mproc.

With Arduino - you choose if you want to use their libraries - nothing stops you from doing direct port access but given a choice, one tends to go the easy route and use the supplied libraries simply because they work. There's a zillion Arduino apps that happily tolerate the slow digitalRead/Write functions as most of the time it makes no difference to the overall operation. Of course, there are some instances where you want to control the port bits as fast as you can - and you can do this if you so desire. People 'think' they're writing in 'Arduino' language - in reality it is just C/C++ with a load of useful functions.

Here's a little anecdote: In my earlier years I used to write tight cycle counted assembler. AS my projects got bigger, I started running into problems with the code being too rigid - if I wanted to change something, I broke something else. Then I read a book called "Code Complete". In the book it mentions that most of your code rarely executes - it tends to be only specific sections where optimisation might be a benefit. This was a revelation to me - it was obvious, but until I thought about it, I'd not actually considered this. So if you're just turning a relay or led on or off, the speed of the port operation is insignificant - a relay takes in the order of 100ms to turn of or off, so what difference does it make if the port operation takes two cycles or 100? Like most things in life - there is a cost. It's up to you to understand what you are buying and whether the cost is good value or not.

I read somewhere that the engineer's job is not one of being smart but one of economics. One could build an infinitely large bridge that would not fall down in a million years and be expensive or employ an engineer to design a bridge that is adequate for the task. The engineer would apply the required science to ensure the bridge would not fail but yet not be excessive for the task thus saving money.