No problem doing that. Unsure which bike or year you've got but later down the line in the SOHC4 they did this...I assume to satisfy the EPA. My friend's newer Ninja had an aluminum cover pressed over the hole where the IMS is. We just drilled it out to access for a cleaning.
Not sure what they used but I would have used a dremel.
On the CB650 VB46 carbs they also have this tab to prevent turning the mixture screws too far, but they also had a plastic cap on the screw which hit the tab. That plastic cap could just be pulled off so no need for grinding the float bowl. You sure that was necessary?
As for the difference in height in the screws, that may be because the screws are different. But theoretically, as long as the screw tips are the same shape they all should use the same setting and perform the same.
Have you removed all the screws to have a look at them?