If inserts seem easier to you and offer the flexibility at your price point then that will work.
Brightness can be compensated for ("attenuated") by using less current.
Hmmmm....well what other ways are commonly used then? In this case, there are tubes that will shield the LEDs from interfering with each other. Those tubes will extend from the LED pcb to the backside of the front face of the enclosure. On that front face will just be an open "hole" if you will, so it seems like you'd need to put some kind of insert there or else expose your LED/pcb to the elements.
The little plastic bezel on CD drives - or any other equipment - is a light pipe - just a rather shallow one.They are solid, and when they are longer, total internal reflection occurs so that the light is conveyed efficiently. This is much better than a tubular structure.
Shouldn't there be an "insert" or a "lens" that is press-fitted into that hole to keep contaminants out?
That is the whole point. The light pipe is the insert or "lens" or "bezel"; it extends to the face of the panel and it is solid.There is no reason you cannot make them out of acrylic rod (clear or if you must, coloured) of the appropriate diameter (or square section), cut to length and the surfaces polished (using emery paper and the car paintwork "cutting" compound).Yes, I have done it.