Yes. Yes, they have indeed buggered up the configuration. What you have described smacks of a lack of planning and/or understanding.
I've been building and implementing a multi-site SCCM infrastucture for about two years now, and while I can certainly understand the duanting complexity of the SCCM system, the power and flexability is staggering.
Our desktop environments vary wildly in their hardware/software setup, so an image-based OS deployment system like RIS, Ghost, or WDS is completely impractical. The difference between those and SCCM is dramatic. Our server Has the drivers and software for every machine, and applies them intelligently during setup.
SCCM takes a lot of investment of time to get right, but once it is, it's magic. One example is we have a large number of machines with M-Audio soundcards. M-Audio haven't written their drivers correctly, so the OS deployment will install the drivers, but not the software needed to configure them (this is possible, as the Intel Media Graphics Accelorator does this correctly).
To compensate, I have a collection whose membership rule is that the machine has said M-Audio card. I then have a sub-collection whose membership rule is that the machine DOES NOT have the M-Audio software. A Silent install is advertised to that sub collection. These get updated each time the machine performs a scheduled hardware inventory, so it's all completely automated.
The collection rules can be based on any information that can be collected from Active directory, network information or the WMI repository. I've found that the WMI can tell you the serial number off the battery in the laptop, if you know how to ask it!
Sounds like your guys are running the site in mixed-mode rather than native. That's why a second computer account is generated after the OS deployment.
You can avoid inputting the mac address by simply joining the computer to the domain, pushing the SCCM client out, and then adding it to the OS deployment collection. I've done this a few times, but I've often found that OEM Windows install takes so long to do its' initial configuration, it's quicker to input the mac and run a bare-metal deployment via pxe.
Dell are the best for this. Not only do they routinely put the mac on the outside of the packaging, but when you enter the service tag on their site, you can download a CAB file containing all the drivers, which you can import straight into SCCM. No mess, no fuss.
The software suite we install during OS deployment is a pretty standard afair, again, because all the systems are so different. You can create rules during the task sequence that check for variables, but I found it easier to keep that part simple, and have software advertisments based on the computers OU container, group memberships, and the most commonly logged on user.
It doesn't deploy all the software during the initial setup, but we give it to the user, and the silent installs cause no disruption. They just suddenly find a new program in their start menu.