How to reduce drill hole clearance for certain components?
The clearance to holes is the same as clearance to the board outline, because non-PTH holes are considered as part of the outline.

To make some holes have lesser clearance in Eagle, you will need to either replace them with PTH holes, or change the DRC settings for Distance-&gt;Copper/Dimension to be smaller.

If you are changing the DRC settings and still want to maintain clearance on other plains, The easiest way to do this is with two polygons. One across the board set to the isolate you require for the outline, and a second on top of it with a smaller isolate to match what you want around traces/components. The second polygon would be drawn well inside the board outline.

For going with PTH holes, which in the case of your light pipe would be acceptable, you may need to set the annulus of the hole to be quite small if space is an issue. Of course remember than the DRC Restring-&gt;Pads settings limit this minimum value, so you'd have to tweak these to get it to allow a tiny annulus if needed.