Hmm, I weigh and use a phone app to track everything I eat. Protein in my diet comes from many sources (tuna included). I'm constantly adjusting what I'm eating as I see the macro balance in grams of p/c/f to maintain a 40%/40%/20% diet. Don't know what else to say.
Those are never all that accurate to begin with

They offer a good estimate but it's an estimate nonetheless.
Just think of it like this, the closest thing you're going to get to the macros of whey protein powders is going to be tuna. So unless you have been eating 50-60 grams of your protein from
plain ole tuna, there's going to be both a caloric and macro variance to a pretty notable degree. I mean, it could quite possibly be that you've replaced your daily protein macros you initially got from whey with tuna but that would literally mean that the rest of your diet didn't change and that you literally replaced whey with plain ole tuna (just the fish, not the canned stuff).
Just to break down tuna:
3 oz ='s 5 grams of fat, 25 grams of protein, 157 calories.
All I'm trying to point out is that it's not that easy to take out whey and replace it with whole foods which are very similar in macros and caloric content. If you took out 50-60 grams worth of protein from whey usage, to have a truly accurate assessment on the difference between whey and whole foods, you would have to replace it with something that is very close to it in macro and caloric content.
It's very possible that taking out the whey has caused a reduction in bloat/gas but that's due to the nature of dairy and the user's gut flora. Some people just can't deal with dairy all that well and their gut flora is not suitable to process dairy thus causing gas/bloat. Plus such issues are only temporary and doesn't really affect body composition. You can eat a ton of broccoli and be bloated as well from that.