You should teach your dog from a young age that you won’t ever take anything off them, simply swap for something better. And that your presence around food is a good thing, not a bad thing.
Yes, you should leave a dog alone whilst eating, but you should be able to walk around in the same room as their food bowl, and take a forbidden item off of them without them growling/biting.
In an ideal world, yes, you be able to do all of those things, but in reality, you need to work with the dog you have, not the dog you think you have. It's also worth remembering that just a dog tolerating something as a puppy is no guarantee they'll be okay with it as a fully grown adult (with the strength and bite to match).
You can also do all of the "right" things when your dog is a puppy and still end up with a dog that resource guards one day due to (for example) pain, poor eyesight or poor hearing, or just because it's fed up having it's space invaded, or it's tired and having an "off" day.
Therefore best practise is to always leave a dog alone while it eats (or sleeps, or rests) because the risk (being bitten by a guarding dog) doesn't outweigh any benefit.
All dogs should have a quiet, safe place to eat their meals where they don't need to worry about people interrupting them.