Oh that is interesting. I feel like the only way to get a better and more reliable solution to this would be to have the OS generate a hash each time the file changes, and store that in file metadata. This seems like a reasonable feature for an OS to me, but I don't think any OS does this. Also, it would force programs to rely on whichever hashing algorithm the OS uses.
I'm not sure I would want this either tbh. If I have a 10GB file on my filesystem, and I want to fseek to a specific position in the file and just change a single byte, I would probably not want it to re-hash the entire file, which will probably take a minute longer compared to not hashing the file. (Or maybe it's fine and it's fast enough on modern systems to do this every time a file is modified by any program running, I don't know how much this would impact the performance.).
Perhaps a higher resolution timestamp by the OS might help though, for decreasing the chance of a file having the exact same timestamp (unless it was specifically crafted to have been so).