The goal is to use Arduino code that can be used on any board. That means that the code is fully dependent on Arduino libraries and the Arduino build environment.
Trying to make things "better" for no reason is just not right. If you write you own code (for no good reason) then we can not help if you have a problem. If you already start to look for trouble before the board is even running, then you will never finish your project.
If you don't want to rely on Arduino, then you should write all your own libraries and your own code.
Suppose your board is running, and your really want that extra microsecond. That is possible of course. I always look at the OneWire library how they did the low level things. Look for the '__SAMD21G18A__'. But you have to have a very good reason to do that, because it is wrong if you do that for no good reason.