I've never really studied fossils, so I don't know much about those. But personally I don't see how anyone could look at the specific biochemical steps involved in ATP production and not think that it was a process that evolved gradually over time. You can clearly see how organisms used to use some ATP variant, then tweaked it a little, then a little more, and so on. There are all sorts of useless steps that make unnecessary modifications to the molecules involved that used to be part of a previous energy production scheme, but are no longer necessary with the current process. Even though the process changed, some of residual steps are still present – even though they don't really do anything. Sort of the biochemical equivalent of a vestigial organ.