Greetings

You have a hard-requirement of using Ender IO in your sub-system, this causes a conflict when using Ender IO Base (for Ender IO TiC for example) as Ender IO and Ender IO base are two different systems.

https://github.com/Vazkii/Botania for example uses EnderIO but has not hardcoded the requirement thus making it so you can use Ender IO base where necessary.

If you're locally trying out MFFS you can just comment out the relevant lines in the build.gradle (ie these). If you're externally including MFFS as a dependency you can exclude the EnderIO versions it includes with something like this:

compile("com.nekokittygames.mffs:MFFS-version") {
        exclude group: "com.enderio"
}

Theoretically that will exclude all EnderIO related transitive dependencies MFFS has under the expectation that they'll be provided if MFFS actually needs them at runtime.