The current generated config is wrong for Better End/Nether mobs

"disable_specific_egg_drops": {
"betterend:spawn_e": 0,
"betterend:spawn_eg": 0,
"betterend:spawn_egg": 0,
"betterend:spawn_egg_sha": 0,
"betternether:spaw": 0,
"betternether:spawn": 0,
"betternether:spawn_e": 0,
"betternether:spawn_egg_": 0,
"betternether:spawn_egg_hydrogen": 0,
"betternether:spawn_egg_jungl": 0,
"minecraft:allay": 0,
...
}

I've updated the mod for minecraft 1.20.1 which fixes this issue.

Link to new file: https://modrinth.com/mod/enhanced-mob-spawners/version/1.2.6

Bit late to the party, but wanted to check open issues before possibly submitting a dupe since I just started getting the same issue myself.
This seems to happen with a lot of other mods to the point that it's not even really a "mod-conflict" as much as it might be a chance to make a more flexible solution.
At maybe only 7 more lines of codes (maybe even less if I wasn't such a mid programmer) a possible fix for this would be to check if "spawn_egg" is the first set of characters in the string after the colon. if yes, remove the first ten characters after the colon, else default back to removing the last 10 characters. The extra adaptability would make it compatible with a ton of over mods that are already out there, like Alex's Mobs and Caves or the "Better (x)" series as mentioned by OP.

This is now fixed in the patch for mc 1.20.4, I might add the fix to 1.20.1.

Backporting would be awesome since I could add it back to the modpack Im currently playing. Not sure why but the mod community is really vibing with 1.20.1 lol