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Yabel can be used for tracing what the GPU does, but it cannot really prevent a proprietary VGA option rom from doing nasty tricks:

The GPUs in the Lenovo x60 and t60 have a bar that gives access to the whole memory:

Region 1: I/O ports at 50a0 [size=8]

I was told that many other GPU also have that issue.

The way to fix that is to get rid of the proprietary VGA option rom. On some boards it's possible and coreboot has a replacement for it. On some other boards, the kernel can initialize the GPU with or without tricks.