Maybe we're thinking along different lines here. Let me explain in full how the new system works, then if your question isn't answered by this, please try rewording it as I'm not sure what else you might be asking?
Firstly - as mentioned above, if you have existing custom sprites, they will continue to work almost as-is. The only thing that you will need to change - and this will not need to be changed right away, I will leave backwards compatibility code in place for a few versions - is that if you make use of the "xxxxxx_mask.png" files (often used for destruction particles in particular), you'll need to replace this with acheiving the same effect via the recoloring feature. Likewise, new ones can be created in the same way, minus the change to how masking is done.
Lemming sprites can have (and in the case of "default" and "xmas", do have; for custom spritesets, it's up to creators if they want to add support) extra metadata in the scheme.nxmi file that allows them to be recolored. This data specifies a list of source colors, and their associated names. For example, a lemming's hair in the default sprites, without any recoloring, is (RGB hex) 00B000. So there'd be a line in styles/default/lemmings/scheme.nxmi: LEMMING_HAIR x00B000. (Note that the name "LEMMING_HAIR" is arbitrary here, I could have just as easily written "FLAPPY_BIRD x00B000" and it would work, as long as theme files trying to recolor it used the same name; but of course, meaningful and relevant names are a good idea.) These lines go inside a "$COLOR_SWAPS" section. (The name "$RECOLORING" was already in use for the conditional recolors, eg. athlete, zombie, etc colors.)
$COLOR_SWAPS
LEMMING_HAIR x00B000
LEMMING_CLOTHES x4040E0
LEMMING_SKIN xF0D0D0
LEMMING_BUILDER_SACK xF02020
LEMMING_UMBRELLA xB0B000
LEMMING_ZOMBIE_SKIN x808080
LEMMING_ATHLETE_HAIR x4040DF
LEMMING_ATHLETE_CLOTHES x00AF00
LEMMING_SELECTED_CLOTHES xEF2020
$END
Note: This has been combined with actually changing the athlete / etc colors to the above. The difference is not visually noticable from the former setting, but it allows the athlete (/etc) and regular colors to be picked individually.
If a style's theme.nxtm points to "default" for lemming sprites, and doesn't specify any recoloring animation, it will still get the default sprites, as-is. But, style creators will likely already be familiar with specifying a few other colors in the "theme.nxtm" file, such as MASK, MINIMAP, etc. You simply specify lemming recoloring colors in exactly the same way.
For example - whereas currently l2_highland points to its own custom lemming sprites, in the next update it can have the following theme.nxmi file, which points to "default" for the actual sprites, but contains recoloring information:
LEMMINGS default
$COLORS
MASK xD08020
MINIMAP xD08020
BACKGROUND x000000
ONE_WAYS x4040E0
PICKUP_BORDER x60C0FC
PICKUP_INSIDE x0080FC
LEMMING_SKIN xFFFFFF
LEMMING_HAIR xFF6500
LEMMING_CLOTHES x0000CE
LEMMING_BUILDER_SACK x732000
LEMMING_UMBRELLA xEFAA00
LEMMING_ATHLETE_HAIR x0000CE
LEMMING_ATHLETE_CLOTHES xFF6500
$END
Remember, once again - the actual color names are arbitrary. If you're setting up recoloring with custom sprites, you can use any names you want; all that matters is that the same name is used in the source style's "scheme.nxmi" and the target style's "theme.nxtm". I could have instead used the name "BIG_DUCK" instead of "LEMMING_HAIR", and as long as that name was used on both sides (default's scheme.nxmi "$COLOR_SWAPS" section, and l2_highland's theme.nxtm "$COLORS" section), it would work.
In terms of replacing the "xxxxxx_mask.png" files - you'd copy/paste them onto the main graphic, in a unique color (perhaps death magenta, FF00FF). You'd then define a $COLOR_SWAPS entry for this color, using the name "MASK" - yes, you can use "standard" color names as part of this too, although MASK is probably the only one you should do so with (but maybe there's a creative idea I haven't thought of for doing this - at any rate, it would have been extra work to forbid it, so the option's there if anyone finds it to be useful).
So -
If you want a custom set that's just a recolor of default (or xmas) - for example, the L2 sets as they currently are in NL, or Arty's "underwater" or "silhouette" styles - you nuke your "lemmings" folder with the custom sprites, and use the above system instead. You don't need to change anything when a new skill (like the Jumper) gets introduced, because it's just based on recoloring the default ones - and it can easily recolor any new ones that get introduced too.
If you want a custom set that's actually custom - for example, GigaLem's Millas sets - you do things exactly the same way they're done now. The only difference would be that you get rid of the "_mask.png" files, and use recoloring to "MASK" in their place, as described above. Again, support for _mask.png files will be kept (but considered deprecated; so don't use it for any new content after V12.7.0's release) for a few versions to give people time to switch over - it doesn't cause much mess to the code to keep this in place, so it's no problem to do so for a little while.
If you want a base custom set with unique shapes, that's then recolored for several of your styles - my suggestion here would be to create a base style that just has lemming sprites, for example (if we were creating sprites that replaced the lemmings with ducks) you might call this "author_ducks_sprites". This would likely be a style consisting only of lemming sprites; it might not even have a theme file. You'd set up the $COLOR_SWAPS section as above for this style's sprites. Then in your other sets - "author_shadowducks", "author_egyptducks", etc, you'd point to "author_ducks_sprites" for lemming sprites, and specify recoloring in pretty much the same way you would when recoloring from default.