As Zoltan said this has been around for a while. It is the oldest issue on our To Do list and dates from Feb 2014!!!
It has definitely been looked at but no-one has implemented a solution yet.
I think that one approach that has been discussed but not necessarily tried is to replace the layers with the Replace With Other trait, which just swaps one counter for another. This could be tested by a non-coder using the Edit Module function from the VASSAL window. It is very user friendly these days and I would be prepared to help someone get started. Anything that needs to be done can be done using that non-code interface. The best thing would be to start with a nationality that has a smaller set of squads, perhaps the French or the Italian. If we can see it working with one nationality we can apply it to the rest.
For anyone wishing to try this at home, it is important to understand that the different VASL infantry unit counters that appear in a nationality tab are really just copies of the same counter with the layers set to a different starting point. So for example, American 667-666-546-536-347-346-236-226 squads and hs in the counter palette are all copies of the 667 counter. Taking out the layers would change this but those existing copies could be re-purposed to be the new counters. Obviously, there are standalone counters and counters with fewer layers and copies.