Well, all I can say is that all the rules of combat in 1e are in the combat chapter of the 1e DMG.. There isn't a single rule anywhere else (maybe one of the later supplements could be excepted, like OA has rules related to Martial Arts which would have been in the combat chapter had they existed at the time). Those rules themselves may not be clear, in fact Gygax is famous for leaving many things unsaid or providing multiple conflicting interpretations, but the actual rules are in one place in 1e!
Now, there are rules about equipment, for example, that are in other places (IE how much damage does a longsword do, or what AC does leather armor grant) but again, the consistency is there, ALL of those rules fall under equipment, pure and simple, no exceptions.
Looking at the 'flowchart' actually exemplifies this. Everything in the first diagram is on DMG pp60-61. Where things are referenced to other rules sections, it is where there are rules about other things, races, classes, and monsters, which provide input to the surprise rules (IE PC Dex reaction bonus, elf abilities, etc.). Note that this wouldn't even be necessary in a unified system like 4e because the mechanic would simply be part of a more all-encompassing general rule, how to make checks, and so all that would be needed is for the surprise rules to state that Dex is a modifier to the check. I'd further note that the diagram devotes a bunch of space to dealing with various popular interpretations of the rules (IE reducing surprise checks to a % in order to compare different die sizes), which would AGAIN not be needed if 1e was a unified system.
My point seems made though, 1e's rules are actually quite modular and clearly organized. They are not so good in OTHER ways, but I don't agree that organization was a weakness of Gygax's. He seems pretty well-organized to me at least.