At least with inotify, ie, incron, this is just a matter of setting a less stupid watch.
You can ask the kernel to watch for several different specific kinds of fs events, either at the file or directory level.
Detecting when a file is either created, or closed from writing, is no problem at all. Ie, handles the case of writing a file normally, editing a file, and renaming a file into exitence without having opened it for writing (that happened while it had some other name you weren't watching). This would handle unlinking and recreating the same as editing or uploading.
You can watch specifically for the close event only, and even more specifically for close-from-write-mode to detect updates but ignore until the update is done. And at the same time you can also watch for creation, which handles creating a file under some other name and then renaming it into existence under the name you care about without the name you care about ever having a close-from-write event.
That would fire off your script when a filename you were watching was unlinked and re-created instead of edited in-place, and then it's up to your script to handle the case where it's a "new" file that is really just replacing an old file.
I don't even see why that should be any kind of special problem. Are some tools doing something like maintaining ooen file handles or something for every watched file??? That would break by unlink-create, but that would be insane.
Perhaps these wrappers that try to simplify things are as usual just a way to break the thing they are trying to simplify. Just misguided crap.
If the feature is baked into an ide or media server and failing to handle that case, well they don't have to fail to handle that case. The subsystem totally supplies the functionality.
For something random adhoc where you're writing your own incrontab and handler script, it's no problem at all.