Currently, this mod (through Brandon's Core) has a hard dependency on Redstone Flux. Now that it supports Forge Energy, can the dependency on Redstone Flux be changed to a soft dependency, via the @Optional annotation?

Not easily because the entire energy back end is based on RF with FE patched on top as a backup power system. But if i ever need to do a complete re write of the power system i will probably make this change.

Would you accept a PR for it?

Its something i would rather do myself as it would require a large re write of the back end code. I am already planning to re write the entire energy system when i do the DE3 re write so i think this can wait till then. And its not really that big of an issue.