If I'm understanding your question correctly, the MD5 is not a qualifier to say the backup you just made is totally complete and perfect in every way such that it will work for you when you try it later.
The purpose of an MD5 for our use is more so to ensure there has been no tampering or data loss in a given file
following a transfer of said file between two or more mediums.
So for example if you made a backup, you check the Md5 and write it down for future use. You then upload that file to a cloud server such as Dropbox, Mega, etc or maybe you even transfer the backup to the hard drive on your PC. Then at a later time, you need that file so you download it through the "series of tubes"

within the internet or maybe you transfer it from the PC through the USB cable to the phone. After receiving the file, you check the MD5 to make sure that it matches, thereby ensuring that every byte in that file is exactly the same as when you created it. That's what the MD5 brings to the table: verification of exactness.
So if you did a backup and unbeknownst to you, it was a bad backup - maybe a partial backup or missing a key component(s), it would still generate an MD5. But knowing that MD5 doesn't change the fact it's a bad backup.
So how could you absolutely know if every single backup you make is good and will work when you try to restore? I'm not even sure that's possible to be honest. I've always just looked at the size and compared it to other backups on the same device. If they're close in size, it's probably good. If one backup is 120 MB and the rest are 3.5 GB, then you can pretty much say you have a bad one.