It wasn’t ever proven but just about everyone in F1 thinks Benetton were cheating, at least in 1994.
From what I understand, it's believed now that Senna was simply wrong about Schumacher using traction control in-race, because not only was Schumacher's driving style rather different to what others were doing, but also he had the advantage of being able to use left foot braking with the semi-automatic gearboxes. Essentially, he (and Mika) were able to more or less create some form of traction control that way, whereas poorer drivers (Verstappen, Brundle) just didn't have the skill to do it. There were only two teams using two pedals that season, so Senna had no way of knowing how these cars actually worked.
There's quite a lot of well sourced evidence that the combination of left foot braking and the greater control it gave over the car in the corners was what misled Senna into believing that it was traction control in use. I believe Senna when he said that something was wrong about the engine noise, but if he had no experience with left foot braking, it's easy to understand why he would think that it was traction control. When you combine it with the fact that the Williams was a pig of a car and Benneton had better aero, it's easy to see why Senna believed that the Schumacher car was cheating.
One other thing that emerged was that Benneton were using a legal form of traction control:
https://www.linkedin.com/pulse/how-rotational-inertia-led-traction-control-willem-toet/ - but this was legal, it just wrecked engines. If you combine this with left foot braking, it's likely that Senna did hear something, he just didn't know the specifics. There's also the point that Schumacher's own driving style involved bringing the car to the point where he actually started losing control, only to regain control of the car straight away. This was different to most drivers, who would estimate where the limit was and aim to stay just under it. I'd actually say that with Schumacher's skill and the brilliance of this system, it's easy to see why he was the fastest driver on the grid that season. It also seems that Schumacher was simply fast enough to unlock all the potential of the aero, whereas Jos simply wasn't.
On the other hand, Benneton's nonsense about launch control code was just that, nonsense. Even in 1994 with ancient software development tools, it would have been easy to remove the code or to make sure that it couldn't be used at all. My gut feeling is that while the process of selecting it wasn't easy, Schumacher was the kind of driver who could and would practice it until he could do it every single time. Yes, the FIA couldn't prove it was used, but I'd be willing to bet that it was.
The fuel filter was textbook cheating, and there's nothing more to it.