That reminds me of something: On the lemmings file archive all level packs are used for Custom lemmings. Personally, I don't like that idea anymore. I wish that the level pack downloads were split into different categories like: Levels which are specifically used for Oh No more lemmings graphics or Holiday lemmings.
I'm not sure I fully understand what you mean. Are you referring to level packs that need to be played in the ONML program rather than CustLemm, because it uses ONML's graphics set numbering rather than CustLemm's? (eg. Brick is set #0 rather than #5) The rest of this post assumes this interpretation.
I think it was like that because most levelpacks are set up for Custom lemmings to begin with, for the obvious reason that Custom Lemmings had been set up to offer all 9 graphics sets together, and the ordering of levels in the levelpack translates directly to the order they will be played in the actual game.
Remember that before the days of Lemmix, if your levelpack is to be played in DOS Lemmings, ONML, or Holiday Lemmings rather than in CustLemm, you can't just copy the levelpack file directly to one of the levelXXX.dat or dlvlXXX.dat files. Well you can, but people will have a hard time finding your levels, because in those games, consecutive levels usually don't fall into the same levelpack file (eg. Fun 1 and Fun 2 are stored in different files).
So really, you should be designing your levels from the outset with CustLemm's graphics set numbering, so that they can be played most easily by everyone. Don't assume everyone use Lemmix.