Simple, for starters there aren’t many ways to Assassinate Chad Bingham, and certain aspects of the level point to the hottub being the main way to kill bingham, with the mysterious additional female assassin target being in one of the major paths to be able to shoot out the hot tub. You also forget that 47’s initial attempt to kill Lee Hong went wrong, and resulted in the death of Tzun (or Zhun depending on which game you are playing)
However more directly there is evidence that 47 did kill multiple people and in fact does sometimes make mistakes, he may be the perfect person, but that doesn’t mean everything always goes perfectly for him:
“In the level “one of a kind” [in Hitman absolution], there is a newspaper article displayed on a wall about the Bingham-de Havilland assassination. It shows a clear photograph of Agent 47’s face along with reports of four additional deaths and one other injury, showing that Agent 47 will sometimes “slip up” in his missions”
Not to mention you are forgetting the level that most directly proves that 47 kills nontargets: Death of a showman. Sure it may be TECHNICALLY possible to complete death of a showman Silent assassin (and the one newspaper in the cutscene may say silent assassin regardless of how one completes the mission), however it is clearly not how it went down as the tutorial and level design points towards one way of completing most of the obstacles (resulting in the killing of numerous nontargets), and not to mention the only way to get silent assassin on the level requires the use of nontarget accident kills anyways.
This also reminds me of Bjarkov Bomb in Hitman: Contracts, 47 100% kills the 3 hazmat wearing bomb-makers and about 2-3 soldiers when he detonates the nuclear submarine. That is absolutely 100% indisputably canon, there is physically no way in-game to avoid those deaths. There’s also Sturrocks brother as well who is likely killed by 47.
There’s also the whole scenario of The Asylum, in Codename 47 he does kill Kovaks primarily because of his own suffering, and quickly dismisses the contractual reason for the elimination, 47 also kills some asylum staff / SWAT members as shown in Hitman 2: Silent Assassin with the opening cinematic (as well as I think 2 asylum staff members in ‘meet your brother’), the aftermath shown in contracts also indicates the possibility that some asylum staff members were also killed by 47.
The map is called Situs Inversus because that’s the main setup for the contract and reason for both Soder’s betrayal and inevitable death. The name “the showstopper” doesn’t really appear anywhere else in the mission, and dropping the light rig onto Novikov certainly stops the show…
47 could have been standing right in front of Novikov when the light rig dropped IF he planted a bomb on the winch (there is a remote explosive nearby in the attic) which is actually showcased as a way of executing the kill in the trailer for Hitman 2016. We see the robot arms killing soders from up close because isn’t a way to change perspective in the space in which the flashback occurs (you would somehow have to move players up in elevation without them noticing and in a way that wouldn’t look goofy, not to mention it would be pretty disorienting to players as well.
Overall, it doesn’t indicate that these ARENT the canon kills, just that the assets are reused in this circumstance in a way that fits better into the sequence.