Did you noticed that pre-Euro coins from Luxembourg have all other catalog numbers than those of Standard Catalog of World Coins? I think it should be KM # for all coins first (if exists) as for other countries and after that other catalog numbers.
Well, it is up to referee which system he (or she) chooses. The L reference for Luxembourg goes way further than KM or MB numbering, so it connects old Luxembourg coins with newer ones. For some countries, KM is making less sense.
First reference is the sorting one, and it is up to referee to make it such way it makes sense when sorted.
A lot of countries' coins appear to have Y numbers as primary (notably Russia - Empire), which IMHO makes a lot less sense.
But really, whatever the referee prefers. I have no problem with using a system that also includes very old coins to refer to modern ones, as long as it doesn't produce hilarity like a page for each year (admittedly this is actually more common for older coins - I still can't figure out why each year and mint of PLC coins seems to have its own page).