Here are the offensive winning percentages for NL 3B men for different periods. Data from the Lee Sinins Complete baseball encyclopedia.
Santo had .618 from 1961-70. He was about 9% of the total, so without him it was probably about .506. Nothing unusual. The guys Santo got compared to were not sub par in hitting.
Santo lead the NL 4 straight years in Total Zone Runs (fielding) for 3rd basemen (from Baseball Reference). But his total over those 4 years, 39, is one of the lowest (BR starts this stat in the early 1950s-I calculated the cumulative total of the leaders over each 4 year period regardless of who it was). It is tied for the 7th lowest in the NL. The lowest is 35 and some of the periods that were lower include the 1981 strike year. The average cumulative 4 year total for the leaders was about 55 in the NL and 72 in the AL. Only two periods in the AL were below 40.
So it is possible that in some years Santo benefits by being compared to poor fielding 3rd basemen. But this is probably not alot of his overall value.
See Yearly League Leaders & Records for Total Zone Runs as 3B at BR. Santo's numbers from 1965-8, the years he lead, seem low compared to the AL in those years and the NL in the years both before and after.