Hello Toshishisa,
The reset value of the register in reference manual is the value before ROM code. Therefore, the register value you see in debugger is the value after ROM code runs. Therefore, it is normal that the register value obtained by deugger is different from the reset value.
If you have any problems, you can reconfigure the register to the value you need in u-boot or kernel.
Have a nice day!
BR,
Weidong