People who aren't antisemites usually don't deny the holocaust when they update the death count based on historical facts. This is called revisionism, not denial. However, it's without much risk of being branded a holocaust denier or revisionist by claiming that the actual number of people having been exterminated is off my say a couple of hundred thousands, wether because of double counting across borders or something along these lines. Since there's existing evidence already proving that at least x amount of Jews was killed throughout WW2 by Germany or it's allies, it's difficult to come up with a number that's way below the official numbers. As long as you're not outright claiming that Jews weren't exterminated or that the number is so low that Nazi ideology shouldn't be judged based on the death count of the holocaust alone, you're free to so without ending up as a persona non grata.

tl;dr: this is a law designed to protect Jewish survivors from having to endure "public debate" about the actual numbers of their ancestors being killed off by a regime. It's not meant to make it impossible to update the numbers based on newly surfaced facts.

Wolfenstein not being allowed to show Swastikas was indeed pretty stupid but that's what you can when you have a conservative majority in the Bundestag. If someone with a gun who also sometimes played ego shooters kills some people because of insanity, you don't want to be the politician who embraced video games and lifted stupid restrictions for them.