Another way of saying this is, you can either create a modified r8168/9.ko for the core, OR the MD, OR both. Once you have compiled it, you can replace it in the core's directory structure or the disless image's directory structure or both depending on what you are trying to do. As Dale says, if you have not mod'd the module then you are not using that chipset on the core and so it doesn't matter if you change the core's version as that module isn't being used anyway.