If it bothers you, pull it off and go to a Home Depot or similar store and look around for something that's see-through red or yellow plastic with a lower profile that will work. I do that all the time, looking for parts to adapt to kitbash something for use around the house or with trains.
Depending on what you find when you take off the strobe cover, you may want to find something that's the same diameter to cover the opening/missing paint or whatever. But at least you might be able to find a lens that has isn't as tall. I know there's a piece in Legos that could possibly work (a red clear plastic piece), but that may not be something you have around. I think I would try Radio Shack and look at various small light switches that have red and yellow indicator lens that you can remove. One of these might be a good size for the replacement. Home Depot etc. may have these things as well.