I went ahead and ground the leds. No sense in ruining perfectly good keycaps
Ah, Penumbra.. My favourite set.
Can't see too clearly from the picture, but it looks like the LED's could be sitting too high because they are the wrong type (have a lip at the bottom). SA caps fit fine on my board with the "without flange" type of 3mm LEDs.
The lighting will not be affected much by grinding. The "lens" of the LED is meant to focus the light a bit more narrowly from the top of the LED, so without it it'll spread more, but only noticable with really clear backlit keycaps.