I deal with quite a bit of purchasing and of course network support. While I see what the OP is trying to justify, I would still agree with Spidey.
I understand the overall project costs need to get pushed down, but there are things they need to factor in that are harder to quantify.
1. Updating drivers, finding updated drivers. Custom, you first have to identify what part was used and find each individual component, keep track of said components, and visit each site to check for updates. Pre-built, you go to a single site to do all of this.
2. Keeping track of hardware inventories. Often the boon of any IT office's lives. Now you have to keep track of each individual component and it's age as well as the normal tracking of location and what part of it's life cycle it is in.
3. My company primarily deals with Dell. (but all the major players have teh same service) Since we buy larger quantities like yours ( about 30 machines at a time) we often get huge price breaks from them. After buying the gold support, which was about 50 a machine, they came out to about a grand a peice. A monitor for another 180 bucks. If something fails, we just call our gold number support line, tell them the problem, they overnight a new part and we ship the dead one back. With newegg warranty, you will have to buy a new part and pay for your own overnight and then you will have an extra part when the process is finished. Or you can just wait for the RMA to finish. If you go this route, not only are you losing the money on your time, but the time on the employee's job too.
4. It also puts all the strain on your office. If you are sick or on vacation, your company is screwed. With a major pre-built group, such as Dell, they can give a service tag and the tech already knows what parts on in it, who to send to, etc, regardless of who is reading the tag. And from personal experience, the gold number is a different level of service. They do not waste your time with "Try this, then this". They understand you are IT and they will just send you the part you request.
5. While I am pretty quick with diagnosing hardware issues, there are a couple that do plague me. Perhaps not 16 hours plague, but more then just a clicking hard drive or something. In the Gold warranty support, it doesn't matter. I just request a whole new machine and they overnight it, and I send the entire thing back. I can just pull the HD sometimes and plop it into the one that just arrived and the end user doesn't even notice a change. You may or may not be able to do that with a custom, since they move so much faster technology wise. Your mother board might not even be made anymore, so you get the next closest thing. If this is the case, you get to reload the OS from scratch and all the apps, since your image no longer represents what your hardware is. You also have to now put a footnote in that you have 43 computers that are identical, but Sally's is now different. Which increases the numbers of things to keep track of, and increases of problem 1, more time on your part used.
So with these things in mind, I could have probably built the things myself for about 800-ish with the same price monitor, but then the extra service I get and the money lost in my time and the emloyee's time justifies it. I also vote call CDW/Dell, and find out what they can do for you.
Overall, while I see that it might take a while to "recover" and justify the cost discrepency, it still makes more sense to just buy them already built. Spidey isn't just talking out of his a$$, but he has a good overall picture of cost of ownership. Not to mention, it is puts the department into depending on you and your skills. What would happen to them if you found a new job? Would the next guy be as good? Generally speaking, it is best to set things up in a standard manner, so if you left, anyone in IT could take your place and not miss a beat.