A Quadra 700 which has been clocked differently than it’s stock clock speed will fail to run Apple A/UX operating system. Generally that would be the only drawback.
I believe overclocking it changes the returned Gestalt value, resulting in some oddities like described above. There may be other issues relating to booting or installing certain Mac OS versions as a result.
Thankfully the biggest issue with everyday operations on a Q700 is just overclocking too much. 33 was my limit before losing features, system stability, but your mileage may vary.
I can't speak to A/UX in depth. I managed to get version 3 completely installed on mine, however I was unable to keep it running after several bootings due to a degenerative spinning HDD malady. I'll be happy to proven wrong with other examples, as I'm simply one witness.
The Gestalt ID problem is more a concern for 040 Macs where a) board resistors' effects on gestalt and frequency/driver value are interconnected (475/605) and b) where board resistors change the gestalt only, but that in turn changes memory timings from ROM and prevents POSTing or booting at higher frequencies (650/800)
I haven't looked into the 63x/64x Macs, but they appear to follow a derivative process that of the 475/605.
MacKilroy is correct though, that these unused gestalt IDs fail in operations where the system enabler doesn't have those IDs.
The gestalt does not change on a 700, as far as I've used it.