apt doesn't assume that you have a reliable filesystem. It assumes that you might crash at any moment, and it would be really important for you to have a consistent view of what packages are installed when you reboot.
But ext3 and more advanced filesystems have been around for almost twenty years now... it seems an odd assumption that your filesystem is unreliable on any machine that isn't completely ancient (is anyone still using ext2, for instance?)
It's not about the filesystem being "unreliable". It's about having the package manager's state checkpointed so that it can recover and resume if there is e.g. power loss or any other form of interruption at any point during package installation, upgrade, removal etc. This means having all of the updated files synched on disc plus the database state which describes it.
When you move to a more advanced setup such as ZFS clones, you could do the full upgrade with a cloned snapshot, and swap it with the original once the changes were complete. This would avoid the need for all intermediate syncs--if there's a problem, you can simply restart from the starting point and throw all the intermediate state away.
Debian calls itself "the universal operating system" and officially supports not only multiple init systems, but multiple kernels (kfreebsd); somehow I don't see it relying on specific filesystems.
