I'll try to explain
Your root filesystem is of some type: ext3, xfs or a different one. If your new kernel has support for the right filesystem, everything should be fine. When you forget to include the support, or add support for a different version of the same filesystem (it's rarely possible, but still), it may not work.
In general, there may be differences in the way different kernels handle the same filesystem, but they are rather invisible for the user.