Macbook pro default maximum screen size does not cover the bottom inch

Kind of frustrated by my new macbook pro.
At the bottom of the screen, there's the icon bar (icon dock), which is about inch height. I adjusted it to smaller size, about half inch. This is what I did, not sure if related to my problem.
At the beginning, I thought it was Safari's problem. Later I found all programs has the problem. I'll use Safari as example to describe the problem though.
When I open Safari, it does not expand to the bottom inch of the screen, as if the icon dock prevents it expanding to the icon bar area of original icon bar size (i.e., inch, not half inch I'm using), and as if there was a line at the bottom inch. I click the plus sign (maximum screen), it still leave the inch uncovered. However, if I use full screen modle, Safari would covers the whole screen.
when not in full screen model, I can drag the bottom edge of Safari, but can only drag to the virtual icon bar line (at bottom inch position). When bottom edge is at the virtual line, the drag arrow is single direction pointing to up. However, I could move Safari to lower and cover the bottom inch area (with icon bar on the top), and then drag the top edge to make it cover all screen area.
What makes more annoying is if a new tab automatically opens, Safari will goes to the size with the bottom inch uncovered. This problem does not happen if program runs in full screen model.
I tried a few programs, all have such problem. Looks to me default maximum screen size excludes the bottom inch (because by default that area is supposed to be occupied by icon bar although I changed the size or just simply hide the icon bar).
Anyone know why? How to solve the problem? TIA.

called Apple, the solution is:
1, turn on sound
2, shutdown
3, press and hold these four keys the same time: left option, left command, R, and P
4, press and release power button to restart
5, after first starting chime sound, continue hold those four keys
6, after second starting chime sound, release keys
this resets some settings --- not sure what is reset though.

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