When both Actually Additions and Lithium are enabled on the server side the server crashes when generating villages.
Deactivating either one resolves the generation issue (using a fixed seed).

Logfile:
crash.log

Have you reported this to Lithium?

No, should I?

Further down the crash log there is a notice about the AtomicReconstructorClass specifically:
"-- class java.lang.RuntimeException when getting declared methods. --
Details:
Analyzed class: de.ellpeck.actuallyadditions.mod.blocks.BlockAtomicReconstructor
Analyzed method name: entityInside
Analyzed method args: [Ljava.lang.Class;@286edb66"

so I thought It would be appropriate to report here.

The issue is, the crash logs produced by Lithium are not useful at all

Can confirm that the problem does not come up anymore.
Thanks for the fix.