Of course there are less expensive ways to acquire/build tools for guitar making. You can make a guitar with very limited tools if necessary. That doesn't mean one always should do so. Stew-mac isn't about the cheapest answer, but about service and convenience ... which you will find much more reasonably priced the more you use it.
For example, why would you buy a hundred dollar diamond fret crowning file when you can get a several dollar triangular file from the local hardware and polish the edges? Because the diamond crowning file does the job a LOT faster and easier. If you have unlimited time, have no budget, or only plan to work on one or two guitars, you should go the inexpensive route with common tools. But don't discount the value of your time. A lot of those tools are worth every penny, and would cost just as much to build if you place any value on the time involved. (Yes there are some plain-out rip-offs too.)
You'd be hard pressed to find someone who doesn't think his diamond crowning file is worth every penny, and would set it aside to use a triangle file.
As for the kits, I do agree that the kit contents aren't always the best choices. I'd say pick the special tools you really need -- or give you particular value -- and keep the rest fairly simple. You will learn what other tools you need/want as you go.