You were, of course, correct. It turns out that my board had the boot0 pin pulled low by default, instead of high. The programming utility would write to flash and verify, but complete process would fail. I fixed this in hardaware, and now everything behaves as it should (including the oscillator).
Thank you for your assitance! I've learned a lot about ChibiOS and the toolchain trying to debug this.
STM32F303CBT6 ChibiOS support
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