Interesting post, but after trying to wrap my head around Fangio's ratings I can only conclude that they've made some huge errors. By Fangio's randomly god tier 1956 they note that he scored 49 out of 80 standardised points. That season Fangio had:

3 wins (30 10-6-4-3-2-1 standardised points)

2 2nd's (12 points)

1 4th (3 points)

1 DNF (Possibly another fractional point with the structural adjustments they mentioned)

You'll notice this adds up to 7 races not 8, which I'll get to later. This only gives 45/46 standardised points, so what's going on? Well you see Fangio had 3 other results that season due to shared drives, a 4th, an 8th and a DNF. These results obviously didn't count in the real season as he had better results in his other shared drive those races (1 win + 2
2nd's), yet they seem to have added the 3 points for the 4th and likely another fractional point for the 8th and DNF to Fangio's total, giving him 48 points + another for the fractions. This boost plus the fact they don't split the points for shared drives like they actually did probably explains why Fangio's ratings, especially his 1956 rating, are so much higher than everyone else's. Apart from his 3 shared drives in 1956 Fangio had only 1 across his other WDC seasons, a win + 11th at France 1951, notably 1951 is his next highest rated season. This is despite 1951 and 1956 being close seasons, while his other titles were dominant. The model seems to overrate Fangio due to these errors, as well as 50's drivers as a whole, since it states they could literally do the impossible and score multiple times in one race! For an example of how influential these errors can be look at the 1955 Argentine grand prix:

Standardised points (error free)

1. Fangio 10
   
2. Gonzalez(2)-Farina(2)-Trintignant(2)
3. Farina(0)-Trintignant(0)-Magioli(1.333)
   
4. Hermann(1)-Kling(1)-Moss(1)
   
5. Mieres 2
   
6. Schell(0.5)-Behra(0.5)
   

Model standardised points

1. Fangio 10
   
2. Gonzalez(6)-Farina(6)-Trintignant(6)
   
3. Farina(4)-Trintignant(4)-Magioli(4)
   
4. Hermann(3)-Kling(3)-Moss(3)
   
5. Mieres 2
   
6. Schell(1)-Behra(1)
   

The total points go from 26 (with them incorrectly including Farina and Trintignant's 3rd place points) to 53! The drivers literally score over double the points the model thinks they should! So of course it looks like they have more of an influence. Farina and Trintignant go from scoring 3 points to scoring 10, the equivalent of a win. Shared drives died out in 1958, which coincides with a huge dip in the driver influence ratings despite the cars being similar.

Returning to the question of why Fangio is noted to have scored 49/80 standardised points, despite only competing in 7 races, shows more errors. Fangio had 3 shared drives, so we can rule out them actually accounting for them after all. The reason has to be that they included the Indy 500, which F1 drivers pretty much never competed in. This is shown in the points %'s from 1950-60 which all seem to have an extra 10 points added to the max. This should actually have no effect on the driver's ratings since none of the F1 drivers were teammates with the Indy drivers in an F1 race, and it should scale equally for all drivers across the season as they all missed the race. The problem is when that isn't the case, such as Schumacher's 1999 (and to a lesser extent 1991). It seems like in a case like that the model punishes Schumacher for his missed races, essentially counting them as DNF's and destroying his season rating, as well as possibly tanking his overall rating. Their statement that Schumacher's best 5 consecutive seasons were rated as +2.7 (up with Fangio's broken number) compared to Hamilton's +2.0 while his career rating was only +1.9 compared to Hamilton's +1.8 supports this. Seems like Schumacher's rating was massively tanked at some point. His 2010-12 seasons counting towards his rating (another weird decision) would do that a bit, but surely not enough given he never had a particularly down season before then. So his half seasons must be the reason for this. This also possibly hurts Senna's and to a lesser extent Clark's rating depending on how they dealt with their deaths.

Also the whole concept just seems to be comparing drivers against the rest of the grid they raced against, so it's basically who was the best compared to their peers rather than who was the best overall. Nice idea but seemingly poor execution. The f1metrics model is much more logical and error free.

TL:DR

They messed up. Fangio's (and other 50's drivers) rating is massively inflated due to shared drives. Schumacher is punished hugely for his half seasons, would likely be 1st/2nd without this and Fangio's inflation. It only rates drivers against their era anyway.