It's best to leave him alone when he's eating.It tends to make them anxious about having things taken from them and creates resource guarding behavior.
I totally agree with dogma. While it may be perfectly fine with some dogs, with others you could actually end up creating the problem you think you're trying to prevent by taking away and giving back food. Since you're not necessarily going to know which category your puppy falls into until it's too late and now you've got a problem to fix, it's best to just not do it at all. It sounds like that's already starting to happen.
I like to work on preventing resource guarding by teaching my puppies to give me things, I reward them, and then give the thing back, or something of equal or higher value. Just a few minutes once a day or a couple of times a day is enough. Put it on cue. I use "give", but you can use whatever word you want - "out", "release", "drop it", etc. It works especially well if there's a toy that you can hang onto at the same time, like a tug or stuffed toy. Tug, tug, tug, "give", mark it ("yes!"), reward, tug some more. Rinse/repeat. I do it with chew toys too, like Nylabones, and Benebones, I hold onto one end while they chew, have them stop chewing for a treat then let them chew some more. Because I maintain possession of the item the whole time, I'm not actually taking it away.
I also like to work a little obedience into mealtimes, such as having them sit while I put the bowl down and then release them to eat. If they break the sit, I pick the bowl back up and wait for a sit again. And once I say "okay", the food is theirs! I may drop something special into the bowl while they eat, but I don't mess around in their food or take it away from them and give it back, ever. Enough of this from a young age, and it builds up a bank of trust, so there's no need to guard their valued resources from me.
Another thing I do it teach them to bring me whatever they have - could be their toys, bones, balls. Sometimes it's a pair of eyeglasses puppy stole off the table, or the TV remote, or a potholder. Because I've already built up a strong foundation of bring/praise & reward/give back getting them to bring and give up purloined items isn't usually difficult. I thank them, give a treat if I've got one handy, and the put the item up where they can't get it. This avoids the "keep away" game, where you end up chasing puppy around the house to get it back.
Once in awhile I do still have to grab my dogs, pry open their mouth and grab something out, but because it happens so rarely I've never been growled at or snapped at or anything like that. It's calm and matter of fact, and we move on.