I think a reasonable argument could be made that if it's in the filesystem it's not end-to-end.
ZFS checksumming has served me well..
If you mean "it's not checksumming data not represented in the filesystem, like unpartitioned sectors", well, no one cares about that data, right?
See this post from Jeff Bonwick: https://blogs.oracle.com/bonwick/entry/zfs_end_to_end_data
Basically, the filesystem isn't the end point, and thus simply isn't positioned to really provide "end-to-end" protection.
Also, ZFS only has it's claims to data integrity if you use ECC memory.
BTW, anything running on top of the machine is going to be vulnerable to your example, i.e. if you have a program that checksums something, and then writes it to disk, there is opportunity for corruption while it's reading the data to checksum it.