A bit simplified but:
When you build a kernel, you get a zImage, this contains only the base kernel files, modules will need to be loaded after loading that base image. If the custom kernel is the same name as the stock kernel, it will use the stock modules, if these are incompatible, it will go into a boot loop till you replace either the modules, or reflash the stock kernel.
Same happens if the modules are missing.

As an end user, you don't need to worry about this.