Based on the package markings, it looks like the CPU was actually lifted from a GBA SP PCB. This makes sense, of course, and neatly side-steps a bunch of potential issues around firmware, bringup, etc.
I know the author says "the CPU is taken from a GBA SP" in the text, but that could also have meant taken from the design as opposed to the specific physical part having been taken.
As you said, it would be more trouble than it's worth to use, say, an FPGA in place of an original AGB-CPU part. Additionally, our part of the community has an appreciation for the original hardware and components; it's more about being able to rescue parts from damaged PCBs and/or push those original components beyond what Nintendo settled on.
Definitely! Obviously it does increase the complexity of the project for others, knowing that you need a donor system from which to desolder key components. But it's great to end up with a product that's the real system running real cartridges and not a Linux computer running emulation.
That said, it's cool that projects like MiSTer exist, and I could imagine that that might be a nice middle-ground for some people— being closer to the real hardware than purely software emulation, but also something that can also be built from scratch with new, off-the-shelf components.
I know the author says "the CPU is taken from a GBA SP" in the text, but that could also have meant taken from the design as opposed to the specific physical part having been taken.