You are in luck - overlayfs provides exactly what you want. Assuming I am understanding you correctly.
When you access (e.g. open) a file (not a directory) in a read-only mode which doesn't exist in the upper layer, you get exactly the file from the lower layer. If you fstat the file descriptor it will look exactly like the lower-layer file - st_dev, st_ino and all. It really is the lower-level file.
So much so that if someone else opens the file for 'write', it will get copied into the upper layer and they will get a handle on the file in the upper layer which they can then change, but you will still have a handle on the lower level file which, of course, will not see those changes.