MTP (Media Transfer Protocol) is junk and unreliable. Don't use MTP unless you just want to pull 1 file. For backups, use a real tool and get the original files.
When doing an MTP transfer, there is a conversion layer (com.apple.photos.ImageConversionService, com.apple.photos.VideoConversionService) on iOS that is converting the original HEIC files into JPGs. MTP does not even give the original file. It actually creates the file on-the-fly for MTP, so for a converted JPG, it's a newly created file with an incorrect "date created" metadata.
Forget about backing up with MTP. You are not backing up the original file in the first place, let alone the correct metadata, so the file hashes won't match. However, MP4s are original (file hashes match), but the filenames are random (does not match on file system). The same random filenames apply to 3rd-party files added to the DCIM.
Here's how to get the original files:
If you are jailbroken, you can SSH and do an SFTP file transfer from `/var/mobile/Media/DCIM` over the network. Simple for grabbing a file without plugging in a cable.
With or without jailbreak but with a USB cable, you can use some 3rd-party tools like iMazing (paid) or 3uTools (free) on Windows or ifuse on macOS and Linux.
In 3uTools, go to "iDevice" tab > "Files" in sidebar > "File System (User)" in category tree > "DCIM" in directory list > Right click > Export.
With command-line tool ifuse, the command looks like:
ifuse /mnt/iphone cp -a /mnt/iphone/DCIM/*
It's best to avoid MTP. Use a tool to access the file system.