Based on the prose examples the article gives (the chess/lunch story and the crucifixion/bike race story), it looks like a truly 'pataphysical system wouldn't need IO at all. Instead, you'd have a program of some sort, that was simultaneously doing 'pataphysical computation and mundane computation. In the story of Jesus and the bike race, the narrative never shifts between the story of racing up the hill and the story of Jesus being killed on a cross, the story is both at the same time throughout. By analogy, I suspect the article would like us to consider what kind of system we'd need to construct in order to, I suppose, be a story about a bike race (or something else equally removed from programmer's usual domain) and an application to serve web pages at the same time.
Of course, given 'pataphysic's status as "the science of imaginary solutions" I won't be holding my breath for a 'pataprogrammatical Rails-killer anytime soon, but it's a fun idea.
I did have the thought that if OO is clearly metaphorical, it could be argued that all abstractions within the program are 'pataphysical. That is, we can say "an agent sends a message to another agent" or "the function passes control to the current continuation", and we're actually describing concrete reality in program-land, rather than metaphors for real-world objects.
In that sense, 'pataphysical programming might be more common than we realize.
A "pataphysical program" would be an object diagram which took on a life of its own, loosing all touch with possible implementations, with considerable documentation, a CVS tree, a length license agreement, etc...
Of course, given 'pataphysic's status as "the science of imaginary solutions" I won't be holding my breath for a 'pataprogrammatical Rails-killer anytime soon, but it's a fun idea.