Thats why Direct X was developed in the first place,a standard API that removed the headaches of varying hardware configurations for the game developers. It's just a cop out to say the PC is more difficult to develop for imo.
I think you're really overestimating what Direct X can do if you think it waved a magic wand and configuration issues vanished. Plenty of current titles have varying arrays of issues, whether from the game developers end or from the drivers provided for whatever hardware is causing the conflict. Also, Direct X not only doesn't cover everything, there are also other APIs as well as entirely standalone peripherals.
That also doesn't address then the other things such as SDKs and whatever array of modding tools the developer chooses to provide, the after support given to those tools and the SDK, fully integrated LAN support and now more extraordinarily dedicated server support - the kind of things that if not present, PC gamers ask repeatedly why not. None of those things are options the developers turned off, or something that they can patch or provide after a couple of weeks work. They would require much time, effort and more so, expense for the developers.
Those consoles have been out along time now, the developers, whilst initially voicing concerns over how difficult it may be to produce games on them, have over the years become very good as well as very comfortable with it. The PC hasn't stayed still in that time, new operating systems, new versions of the APIs, endless driver releases for the several new generations of new hardware and then throw into the mix new facets such as SLI/Crossfire which are now popular enough for support to be expected.
Ignoring the idiots who hail the death of PC gaming at every opportunity, PC gamers themselves have to accept that multiplatform games are just what developers are doing now and various sacrifices have had to be made to ensure they can actually do that within the same periods of time. If anything I would see it as quite an amazing feat that within the same time-frame to develop a game now it can come out on potentially several of the consoles and PC near simultaneously, rather than a single platform and perhaps another a year or so later. Even with compromise and all, many of these multiplatform games today aren't ports so many brand them as, especially when you remember the the horrendous crap you would have had 5-10 years ago being re-released on another platform years later with clunky, barely workable UIs and shoddy, unplayable performance (or alternatively you could just play GTA IV, for a recent reminder).