I think this is a good idea, as it allows for labelling. I’ve got so many similar looking bits that if I just put them in an array of holes in a piece of wood I’d easily get them mixed up.
I’m still learning about endmill life expectancy but protecting them from accidental contact can only be a good thing.
I’ve posted this picture elsewhere but I really want to point out that you are making life more difficult for yourself if you don’t have a tool numbering system for your tool library. It makes it very easy to have pre-defined feeds and speeds in programs like Fusion and Vectric (even CC). It also provides you a check because most post processors will use the tool number at the beginning of the program, so when you load and start a program, it will usually remind you to use the correct tool number.
Therefore, my old tool holder looks like this, although I am rapidly outgrowing it and will need a bigger one soon. The lighting is too bright, but you can see that I engraved my tool numbers next to each hole.