For cases where we only need the hole to be perpendicular in one axis, such as from side-to-side, but not front-to-back, then visually lining up a line on the top of the drill with a line on the workpiece seems to be an option.
For example, when pre-drilling the ribs on roofing metal (22 sheets, not all shown in the photo) I needed the hole to be perpendicular from side-to-side so that the holes remained in the peak of the rib. But I wasn't as worried about the holes being perpendicular from front-to-back along the rib (that would have been nice, I just didn't have that luxury).
So, I stood behind the drill and visually lined up a line on the plastic moulding at the end of the drill with the rib line behind the drill. I also kept an eye on the line formed by the drill bit.

That worked well. All of the holes were within the peak of the rib.
With that said, this might not be accurate enough for thicker workpieces.
Edit:
Punching instead of drilling might have been a better option:
How to Build a Garage #6 Metal Siding - RR Buildings (YouTube 7:31)