I've moved away from bezels as well. (they are big, clunky, and serve no purpose...most don't even hold the LED solidly in place)
I started making little "LED boards".

The hole for the LED in the board is just large enough to allow the top portion of the LED through, but stops at the bottom "ring" of the LED.
The LED is inserted in the board hole on the trace side and soldered to the closest pads.
The thickness of the PC board coupled with the thickness of a standard enclosure puts the LED protruding through the enclosure at an ideal depth. (This is for 3mm LEDs. A 5mm LED would need additional board shims to achieve the correct depth)
The non copper side of the board is glued with adhesive (your choice....epoxy, gorilla glue, etc.) to the enclosure making a good, solid connection.
Off board wires are soldered to the trace side of the LED board. The wires can then be routed to switches, LFOs, power. etc.
You can make up a bunch of these boards in a few hours and keep them on hand for future projects.