Sure. But "with a nearly perfect on-time performance of 99.3% on Hudson, Harlem, and New Haven Lines," there isn't much room to hide problems. (LIRR is 96.3%.)
The point is we have systems that have been well built and well maintained. They just don't get coverage because they just work. (The LIRR is far from perfect, mind you. But it's apparently outperforming the DB. You have to get to some of the worst routes during peak conditions to get in the neighbourhood of DB's systemic numbers.)
I deal with late trains around two-thirds of my trips. Sometimes up to two hours of delay.
SBB CFF FFS has similar numbers, except it defines "on time" as "within 3 minutes"[1] which is of course harder to achieve.
[1] https://company.sbb.ch/en/the-company/responsibility-society...
I bet, however, it's not uniformly distributed and some lines are late more than others.
Hopefully that 95% is them being honest about the current state, while they push higher.