Yup. Agree with the above. It's an issue of the number of warm bodies capable of repairing. You never want to rely on the gunner for repairs, but he should always be available to help out wherever needed. Thats why gunners tend to take Pipe. Versatility of 'in a pinch repairs'. Maybe he's keeping the balloon up while both engineers are camping hull, maybe just tapping his gun during tar/sand.
If you put the buff on the gunner, one of the engineers is gonna have to run around like a madman trying to be in two or three places at once. Not to mention, during heavy "oh crap" moment repairs, guns are fairly low priority. So while the second engineer is running around trying to help on hull, keep engines up, and rebuild balloon, the gun is basically going to go down guaranteed. At that point, the buff gunner is 100% ineffective. This is the worst situation. Having a memeber of your crew that literally cannot do anything helpful.
Now, if you want to have the main 'gunner' buffing consistantly, I highly recommend 3 engineers, 2 standard 1 buff. Buff engineer will treat his role as though he's a gunner, only jumping off the gun during heavy repairs. Buff the engines and hull once on your way to gun, and focus on buffed gun. When he's off the gun, he has the ability to maintain his area (gun, possibly engine/balloon), while the secondary engineer with a full kit will be able to handle the situation that much faster, and relieve the gunning engineer of his small repair duties.
3 engineer, 2 buff is definitely way better than buffing gunner, but like Captain N said, it doesn't always work out so well. It lowers the versatility of your crew.
Assuming Pyramidion, with the main engineer on the hull, wrench/buff/fire doing the 'gunning' role, and wrench/buff/extinguisher on balloon/gun. You'll have buffed components, and 2 consistently buffed guns. Oh crap... everything is on fire and your hull engineer is pinned down! The 'gunner' is going to have to go put out fires, at which point your most important gun is not firing. If he's not going to put out the fire, just let the engines burn out, why does he have extinguisher? You're wasting a tool slot. Very not good either way.
So you switch it up. Pyramidion, Mallet/spanner/buff on gun, wrench/buff/extinguisher on balloon. It's pretty much guaranteed that the wrench engineer is going to need some help at some point, or have to spend some serious time camping the balloon. It takes quite a while to either rebuild, or repair from low health with wrench. That means either secondary gun is out of the picture for a portion of the match, or the gunner has to occasionally jump over and help with balloon. Very not efficient either way.
Last set up would be to have the engineers swapping out to keep the more important gun buffed and firing. In this setup, you are able to handle fire repairs, balloon repairs, and keep at least the more important gun buffed and firing. Unless you have weapons that both work well with the same ammo type (Gat/Flak is good with both on heavy clip), you're losing out on proper ammo types. With many gun setups (gat/mortar, merc/flak, merc/mortar), one of those guns is going to have to use vanilla ammo half the time. This is clearly the best option, but still not as efficient or easy as 1 buff/gunning engineer.
Any time both guns are not buffed, loaded with the proper ammo, and firing, you're losing the benefit of having 2 buff engineers.