Assume a given pattern has a default height of .25 inches. If you keep that pattern at the original scale and place it on a board at a depth of .4 inches and height of 100, the top of that pattern will be .15 inches below the top of the board (.4 - .25).
If you increase the height to 130, the height of the pattern will stretch to 130% of the original, or .25 X 130% = 0.325. So the top of that pattern will be 0.075 inches below the top of the board (.4 - .325).
If you keep increasing the height eventually you will get to a point where the theoretical top of the pattern is higher than the top of the board. When the pattern reaches the top of the board, Designer is smart enough to not let the pattern go any higher, since there is nothing to carve. Setting a pattern to 999 guarantees that top of the pattern will be at the top of the board. In the previous example, so would setting the height to 150.
If you resize a pattern larger, it's height increases as well, And if you make a pattern smaller, it makes the pattern height smaller.
I also find it confusing there are two heights - the height in designer, which is the % you are asking about, and pattern height, which is the default height of the pattern when it was created.
I posted a pattern I made to play with height and help me figure it out not long ago. It is in
this post. It helped me a lot.