I've been poking around invokedynamic and MethodHandles information recently.
It seems that BOTH Linkage.registerBootstrapMethod() and @BootstrapMethod are deprecated as means of marking bootstrap methods as such.
How are they registered to the constant pool?
As of Java 8, there is no Java language-level support for registering bootstrap methods. Bootstrap methods are registered by a bytecode emitter (source-to-bytecode compiler, bytecode transformer, instrumentation agent, etc.) in the BootstrapMethods attribute in the class file(s) from which they are used by CONSTANT_InvokeDynamic_info values in the constant pool, which are in turn referenced by invokedynamic instructions.