I don't think there's one size fits all answer for all of these examples.
As already mentioned in the early decades of the WCC, only the top scoring car counted, so those earlier examples are probably at least partially down to, for instance, Vanwall in 1958 and Lotus in 1973 having a "number two" driver who would have been team leader at almost any other team, and chipping in with a good share of WCC points in a system where finishing second in a team 1-2 scored the team nothing, and having a poor number two cost a team less, for instance Fittipaldi in 1972 doesn't make the list despite his teammate famously scoring zero points.
By the 1980s both cars scored so a poor number two could drag a WDC-winning team down, Rebaque being the most obvious example of that. To an extent in 1994 too between a raw Verstappen, an injured Lehto and a couple of Herbert DNFs at the end of the season thrown in, although that was also a case of Schumacher winning in the second best car over the course of a season (I'm not going into all the option 13, DQ, suspension arguments..)
1982 and 1999 injuries (or worse) come into play, in 1982 Ferrari would surely have done the double had at least one of Villeneuve or Pironi completed the season. 1999 had Schumacher's broken leg. Was tempted to add 1976 to this category too, although actually looking it up, Lauda was never actually replaced, they either ran 0 or 1 car during his absence, and his "replacement" Reutemann only did one race - in a third car where Lauda made his comeback. Probably more a case of Regazzoni > Mass, with this again being under the best car only scores points system.
1986 is probably the clearest case of the list of a top driver outperforming his machinery over the season.
2008 is kind of all of the above, a top driver in not clearly the best car, an underperforming teammate, and two top drivers at or close to their career peaks racking up the points for Ferrari.
And 1983 is just...weird. The Brabham was quick and I'd have probably ranked Patrese as the best of the number twos in the top three teams that year, quickly glancing over the '83 results he had a LOT of retirements that year, I remember Imola was self-inflicted, not sure off the top of my head how many were mechanical, but that may have cost Brabham that year.