What happens if the PCI voltage in input to a GPU is different from external power supply voltage?
I'm assuming you're asking about 12v power from the PCIe edge connector, and 12v power via one or more 6 pin or 8 pin cables.
If they are directly connected inside the GPU, then there would be a large current flowing from the higher voltage supply to the lower voltage supply, which is likely to damage something. And the highest-voltage supply would see the entire load, which is less than ideal.
However, GPUs do not simply wire these inputs in parallel. Instead, what is usually done is to supply different phases of the core voltage regulators from the various inputs. In this way, the load can be shared more evenly across all of inputs while not directly connecting then to each other, and the regulators can compensate for variations in supply voltage between the various inputs.
Now, I don't have a schematic for a GPU in front of me, but I do have some documentation for an FPGA accelerator card in a GPU form factor (Xilinx VCU1525, precursor to the Alveo U200/U250).  This is the block diagram of all of the voltage regulators on the board:

There are four different power inputs: PCIe 3V3, PCIe 3V3AUX, PCIe 12V, and 12VAUX.  The first three (highlighted in blue) all come from the motherboard via the edge connector.  12V AUX comes from a standard 8 pin PCIe power connector.  As you can see, 12V AUX supplies 5 out of 6 core voltage regulator channels, and there is a FET switch that can switch a few other internal supplies over to the external input.  There are no direct connections between 12V AUX and PCIe 12V.
Additionally, the number of active power supply channels will change, depending on what's connected.  From the manual:

The VCU1525 PCIe CN1 edge connector provides limited 12V power (5.5 amperes max.). The VCCINT power circuit is comprised of six phases to allow a two-step additional power increase when the auxiliary 12V power is applied through the 2x4 power connector JP1, shown on page 17 of the VCU1525 schematic [Ref 7]. JP1 is split into two sections, each with
its own PRSNT detection circuit.
VCCINT power is incrementally increased as follows:

PCIe edge connector 12V power only results in VCCINT phase 1 voltage at 35 amperes max.
Plugging a 4-pin 2x2 12V connector into JP1 pins 1-2-5-6 enables 12V AUX0 recognition, and VCCINT phase 2, 3, and 4 come on (phase 1–4 max. current is 110 amperes).
Plugging an additional 4-pin 2x2 12V connector into JP1 pins 3-4-7-8 enables 12V AUX1 recognition, and VCCINT phase 5 and 6 come on (phase 1–6 max. current is 160 amperes).


Presumably, GPUs will use a similar design so that the power draw can be properly split between the input connections.
Edit: I found a block diagram of the voltage regulators on a 1080 Ti here, it definitely looks like they're doing something very similar:

So, to answer your question: yes, it should be safe, if the card is designed to properly share the load between various inputs.