the docs for the MT7688 are pretty light for a MPU

I would suspect that Mediatek thinks of it not as an MPU, but an SoC designed to be a wifi router or a few related types of media boxes.

Crystals typically have two closely spaced but distinct resonances, and are intended and specified for use at one or the other in compatible type of circuit. The "Xin/Xout" style would likely be operating in a series resonance mode, while the one side grounded would be operating in parallel one. To get an accurate frequency you would need one cut for the resonance mode intended to be used.

If you are designing your own board at more than "see if I can" level you probably need to be in contact with Mediatek - not only for details, but to arrange a supply of chips. For an experiment, just transplant the crystal along with the chip.