It probably costs a lot more than $250,000 to develop a laptop from scratch, so I wouldn't blame them for taking a higher level systems approach and buying in a pre-existing motherboard design. However, doing that inevitably gives up control of the design (which puts into doubt their claims of being completely open). If that's the approach they've taken, they're not particularly open about it.
Novena[1] had a total budget of ~750k$. It was done from scratch, with some nonstandard (and somewhat expensive) components (e.g. an fpga; it had a software defined radio included too, though it was a mostly-off-the-shelf-one).
To design and mass produce a laptop as slim and well integrated as the Purism laptop is significantly more work. To do so having never produced a laptop before would cost even more so. $250,000 really is a small amount of money when you're trying to mass produce cutting edge consumer electronics.
Of course they may (almost certainly do) have other sources of investment.
Much has been written about the fact that Apple controls both hardware and software design. What kind of integrations become possible by combining open-design hardware with OSS software like Linux and Qubes?
Maybe it was chosen because the "high" voltage isn't specified and the standard might say: "Pull down to GND to activate, leave open to keep card off." Then you don't have to think about the internal logic voltage of the circuit, you might fry the card if you pull up to 3v3 if the logic input is only 1.8V tolerant.
If the wires to the switch fail then the card fails on.
The reality is that the chip/firmware/driver combination is tested by turning the power on once and then making it pass a few benchmarks that reviewers like. Doing something new and exciting may or may not work.
Certainly, some drivers are way better than others (ath9k is pretty good), but I imagine they tested the power up/power down method, noted that the kernel panics 1 time in 10, and decided nobody would buy their product if they implemented it that way.
So, yeah, why all the solder and "chip" modifications?
And while the webcam/microphone switches will prevent the particular devices from working, I'm not so sure about the WiFi card and Bluetooth. The microphone surely is dead by cutting the single signal line and the webcam by cutting its power.
But there's no guarantee that the W_DISABLE# pins are honored with every firmware of every possible wifi module that could be inserted into that slot. What if W_DISABLE#, on the card, is only a gpio that is checked by the WiFi chip's firmware? It would have been safer to also cut the power there, too. Or at least to verify that W_DISABLE# cuts off power to the RF PAs (transmitter power amplifier) of WiFi and Bluetooth in a way that can't be circumvented.