ano :
I say it again, you have absolutely no clue where Direct3D and OpenGL fit into the engine's architecture! an engine is not built only and only using DirectX/OpenGL! You're just talking out of your arse, I'm sure you know it yourself very well!
DirectX (Direct3D IS a part of DirectX, NOT the other way around) and OpenGL are INDEED APIs for the graphics end of things. and unless you want to either mess directly with a video card (WAY too much work supporting cards as old as DX9 cards, which is about the level of graphics in the PS3 and XBox 360) THAT is where they fit.
DirectX, using XACT, XACT2, etc, handles the audio. IF you want something easier, then you go and get a license for FMOD, or implement a hit-and-miss OpenAL (if you don't provide some kind of driver interface at installation time.)
On the PC you have either an AMD or INTEL 32bit (x86) CPU (not so likely on new machines, although the OS may still be at that point) or a 64-bit CPU (x64) and OS. They run the SAME code respectively for each mode.
Physics and AI are not directly video related, thus they don't directly deal with the video, but work on objects defined in the world, adjusting properties and behaviors.
Network used to be part of DirectX (and is now depreciated), but once you have a working library or code, the only adjustments ever needed will be for data and communication protocol overhead.
Input can be tricky, but once you have something for that, that never really changes, only what you do with that input.
Now, I think I covered most subsystems of a game engine (excluding scripting). On the PC most of that is unified and seen through the same API, irregardless of what is there... other parts rely on the API and drivers to work.
Now, the PC has two sets of instructions to work with, but have a common 32-bit (x86) to reach for older systems. ALL these platforms are different in hardware, but the PC has more abstraction available. The hardest part of it all is left to having the PC scale the graphics to a higher level, and the inconvenience of a PC player likes their keyboard and mouse over a game controller.
The Problem is: These publishers see consoles as their cash cow, and PC is now that uncle you'd rather forget, except there are enough of us PC gamers left that they can't just ignore us completely. SO they resort to FUD to manipulate the public and investors into abandoning the PC platform by way of selectively burying their heads in the sand on console piracy, unless that pirate makes too much noise to hide (but go back to ignoring once that pirate is shut-down) while spending extra money for servers and DRM that doesn't stop piracy but still costs money (perhaps that is their "overcomplicated" angle... Simple, STOP putting that crap in a game and save that money.)