Depending on the case the bays can be removable. I had to take mine out to my GPU.
Buuuut if the GPU doesn’t fit in the case length wise these massive ass GPUs probably won’t fit height wise either. My 12vhpwr cable is making an uncomfortable ass turn with the side panel on. And it seems like every angled adapter is more house fire than the last so I’ve held off on adapters.

Any tool is just going to blindly read the TDP, add up the TDPs, then add some wiggle room to say if it’s ok or not. The 2060 has a 160w tdp, the 3060 has a 170 watt. You’ll probably be fine unless you were really skimping before. Neither are particularly high power draw cards.
That said the 30 series has a reputation for really high transient spikes of power. Those spikes can easily exceed 200% of the normal power draw. If you have a high quality power supply it shouldn’t be an issue. But if you skimped on the wattage and quality that could be an issue.
But if you’re worried if a GPU is compatible with your motherboard then don’t. PCIe is backwards and forwards compatible. Unless you’re trying to run a 5090 on the first pcie board you shouldn’t have any issues. And even if you did PCIe version compatibility probably aint it. It’s probably only power.