Short answer: Yes and no.
Long answer:
If you add emblems for a fourth character and the mod's wad file includes this character, it will work -- provided you don't add any other characters to the game prior to adding the mod.
As the game starts up, it has the following characters:
0: Sonic
1: Tails
2: Knuckles
Imagine you have a mod which includes Amy Rose as a playable character. When you add this file, the character roster becomes this:
0: Sonic
1: Tails
2: Knuckles
3: Amy
Therefore, if you include emblems tied to Character 3 in the mod's MAINCFG, they will appear for Amy as planned. However, if before you load the mod you add another character wad, let's say, Shadow, the character list becomes this:
0: Sonic
1: Tails
2: Knuckles
3: Shadow
Adding the mod will append Amy to the end of the list, like so:
0: Sonic
1: Tails
2: Knuckles
3: Shadow
4: Amy
However, the MAINCFG is setting emblems for Character 3, so they will appear for Shadow instead of Amy as was originally intended. There is currently no way to avoid this.