I'm still a little fuzzy on the actual nature and function of taking skulls in Khorne's name. Is the severed skull actually bodily transported to the realm of chaos when it is offered up? Or is it like some strange inverted transsubstatiation where the skull "here" is consecrated and a copy/replica is sent to the pile under Khorne's throne? Is this easier or harder when related to the size of the victim? For example when Roghrax Bloodhand attacked hive fleet Kraken to take large and impressive skulls where did Khorne put them? Does he play jenga with them?
There is no physical transfer from one realm to another. Not by simple acts like this. Remember nothing in the warp has any corporeal form. If a mortal were to witness it, his mind may interpret it that way but that's all it is, an interpretation.
The act of decapitation is an act of murder and a rather extreme one. Given that the gods represent emotional extremes, it makes sense that his followers would be driven to this. But it is still an emotional connection to the act that feeds Khorne, not the physical removal of the skull itself.