The PCI-E bus controls most I/O interfaces on a system and many of them, particularly drives, tend to be intolerant of significant deviations from spec. 110MHz will rarely be safe. You aren't likely to damage any hardware, but you could easily experience subtle data corruption or other instabilities.
Underclocking the PCI-E bus is usually easier, but again, running it out of spec may cause issues.
How tolerant a GPU is to out of spec PCI-E is highly variable, but PCI-E clock should have almost no bearing on the power consumption of a GPU. The PCI-E interface will need to work faster or slower, obviously, but this doesn't amount to much on most parts. Some older GPUs used the PCI-E clock as a reference clock which could have unpredictable effects on the card, but I haven't observed this in a long time.
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