No, and there can't be. Rsync uses file timestamps to determine what to copy and what to skip. There's nothing similar at a lower level than files. The data on the disk doesn't remember that there used to be a different partition arrangement.
In order to make sure that two disks are identical, a tool working underneath the filesystem would have to read every block on both sides and copy the source block onto the target block if they differ. That's usually slower than unconditionally doing the copy. It might be faster if writes to the target disk are a lot slower than reads (but still a far cry from what rsync gains by completely skipping unchanged files); I think I've seen a tool that did this but I can't find it now.
If you made a change to the partition setup on one side, make the same change on the other side, then call
rsync on the individual filesystems.