Damn, this is hard to make any clear calls about. OT1H, the look of the new version, as in how well you see the rivet, is a very good rendition of how flush rivets look through pretty fresh paint. OTOH, they also look way too big, being several pixels wide.
I think you're under a msconception as to how riveting works in the aircraft industry. It does NOT deform the skin, at least not intentionally. If it does, then it's a problem and has to be reworked or scrapped.
When you build up a skin panel (consisting of the skin itself and any attached structural members such as stringers), the skin itself is always pre-bent to the curve of that part of the airplane, so it retains that shape naturally. This is not only so it ends up with the aerodynamic shape the designer called for, but also to prevent building stress into the assembly. That's a bad thing because it puts the structure already part-way to its breaking point before the plane leaves the factory, so it can't take as much load as designed in flight. Also, it will try to return to its natural shape, resulting in the structure twisting out of true, ruining aerodynamics and making the plane fly crooked.
For this reason, the outer surface of the skin trumps everything. With the all the parts in the jig, before drilling any holes you have to check for gaps between the structural parts and the inner surface of the skin. If any exist, you have to build shims to fill them. OTOH, if any of the underlying parts stick up too high, you have to file them off or something. IOW, the structure is ALWAYS built to the skin, and the skin is NEVER deformed onto the structure.
Once you've got the parts fitted correctly, you drill the holes, countersink for flush rivets, disassemble, debur, and then reassemble with sealant between the faying surfaces. Only now are you ready to install the rivets.
Rivets are not "shot" into the plane as if by a nail gun, despite "shooting rivets" being the term used in the industry. Instead, rivets are inserted by hand into their holes. They go in quite easily because rivets are designed to be slightly smaller than their holes. This is because they will be "bucked" into final form, which causes their shanks to expand and fill the hole.
The vast bulk of aircraft rivets are bucked in (although this is still called "shooting"). Bucking rivets is a 2-man operation. 1 guy applies a rivet gun (it looks like a drill but it's really a small air-powered jackhammer) to the head and the other guy holds a bucking bar (just a conveniently sized slab of steel) up tight against the tail end. The combined action of the gun hammering the immobile rivet's head, and the pressure of the bucking bar on the other end, expands the rivet's shank to fill its hole and mashes the tail into a thick, button-shaped disc called a buck-head.
During this process, the only thing having pressure applied to it is the rivet. The skin itself has nowhere to go, because the structure is tight up against it, and is itself held firmly in the jig, which is bolted to the factory floor. Thus, you get a nicely bucked rivet without any skin deformation. And the head is absolutly flush with the skin, another thing the inspectors check for on the line. So there's no deformation at all on or around a flush rivet.
NOTE: some rivets are squeezed instead of bucked, but in general that only works on very small assemblies, no bigger than the throat of the squeeze gun. The principle is the same as bucking, but it can be done by 1 man.
That all said, there was (and is) a different method for making flush fasteners. Instead of countersinking the holes, the skin itself is actually deformed by a dimpling machine. It could only be done on very thin metal, and caused a number of problems elsewhere. For instance, the bottom of the dimple stuck down below the inner skin surface, so you either had to have corresponding dimples in the underlying structure, or you had to do a LOT of shimming. Also, the dimpling process tends to deform the panel somewhat, making it very hard to get a good fit on the underlying structure. And the rivet isn't nearly as flush when you get done, anyway. As such, dimpling has only really been used for relatively flat panels, like on wings, where quality isn't as important as quantity and speedy construction. It appears that the Germans started using dimpling towards the end of the war, which is why their rivets are so prominent even when painted over. However, I don't think any Allied combat plane ever used it. It's just not a good option for high-performance planes.
