The microcode update most probably will be given out to motherboard vendors who then will hand it to existing customers with a BIOS update. Users that currently overclock their Skylake CPU should think twice before applying future BIOS updates if they don´t want to lose that possibility.
Also most new motherboards can be expected to incorporate the update, so the overclocking party will soon be limited to older boards.
Since Intel offers overclocking capabilities only on high-end “K series” Skylake CPUs, closing this loophole was a priority for the company.
An Intel spokesperson has justified this move to PC World, stating that overclocking was not recommended for the affected CPUs since they were not built for it.
“The latest update provided to partners includes, among other things, code that aligns with the position that we do not recommend overclocking processors that have not been designed to do so. Additionally, Intel does not warranty the operation of the processor beyond its specifications.”
Since Intel´s warranty does not cover overclocking the K series Skylake CPUs either, it looks more like the update is intended to protect the company's own interests.