You point out an importatnt detail I left out...
Early SMT mfg. lines tended to be extremely unreliable. My take on the whole thing was that if the line engineer for a given line understood what it really took to properly flow paste, and how smooth the pic-n-place line, as well as any conveyance between there and the re-flow oven running smoothly enough that it didn't bounce the heavier IC's out of their less than perfect adhesion to the land provided by the paste, then the solder would flow and whet properly to the lands and leads, and it would be reliable as the PCB itself generally. But wave solder and stuffed through-hole components were tolerant of a large number of PCB assembly sins that SMT isn't.
If the boards get fingerprints all over them going into the line, and the ovens aren't clean enough, or the line bounces components off their pads (even out of registration too far), or the oven's temp profile isn't right, then the solder quality suffers in ways that just didn't matter even on large scales for TH assembly lines (remember the 100% hand stuffed, often in some house-wife's kitchen a few hours each day, then going back to the assembly shop for wave-solder in their hatchback the next day. they generally worked, or at least the solder generally worked.).
Ah the good 'ol days. SMT was thought to be really hard in the beginning, but mostly that seemed to be the opinion of experienced TH assembly folks. Only some of them could see past their years of status-quo methods to understand that things like finger-prints, dust, hair, oil, smoke, or pretty much ANY other contaminate on the parts, the PCB, or in the oven's internal environment really mattered. They matter at any large scale weather or not anyone in QC noticed anything wrong or not.
That's how the military got away with their early ramp of reliable SMT assembly technology in the high reliability segment. They understood the science behind what they were doing, and had the discipline to follow that, and make sure their suppliers did as well.
I'm feeling a little nostalgic now for those 'good 'ol' days when assembly was easy, but computing was hard. :-)