It doesn't give you direct access to the system because a multi-user OS is running on it.

And also because a lot of thing like DMA transfers require contiguous memory which the OS can't guarantee you when do a malloc.

Projects like SPS2 allow you to get pretty close to full hardware access.

Again, the hardware register issue is not Sony crippling the system, just a result of having a multi-user OS run on it.

Sony does prevent (try to) you from using the IOP which limits you from accessing the CD drive/memory cards/etc... but not the EE/VUs or GS