Hi,
I´m quite new to Arduino, too.
But I think you misunderstood "Arduino". Arduino is an IDE and maybe you can call it a "philosopy".
When I read your post you think that "arduino" = "AVR microcontoller". But this is not the case.
With the arduino IDE you may be able to program many different microcontrollers: AVR, ESPxx, ARM,....
So different microcontrollers have different access to their pins, for example. And to avoid that you need to learn all the access modes for each microcontroller individually they built high level functions.
This code: "digitalWrite(3,HIGH);" you can use and it will work with every supported microcontroller.
But this code "PORTD |= B00001000;" just works on one type of microcontroller.
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For sure this all has benefits and drawbacks.
Arduino is simple to use, but also a bit awkward and not that code effective and processing time effective than it could be.
Good thing is you can use an AVR C compiler and don´t need arduino IDE at all.
You may use other assmbler.
You may use Ardunio, just do what you prefer.
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Using Arduino while using very hardware oriented programming style is counter productive in my eyes.
Klaus