Hello Riley, and welcome back to the community!
It’s great to hear that our GPS solution is helping you in the rapid deployment of your Shakes in remote areas.
The timing will be consistent across all channels of your Shake, even if the time is not perfectly synchronized with the NTP servers. The time source inside the Shake is a single one that all channels acquire data from, so as you wrote, a second needs to be a second for the entire site, even if it is off UTC by a second.
There should be no issues with both an expanded storage USB and a dongle. I remember users that have Shakes out in the field that use storages + GPRS/3G dongles without problems. However, if you prefer, you can also consider using a larger-capacity microSD card (although we recommend external USB storage) that can contain all the data you need between each download session. You can find an estimate of the required capacity here: Commonly Asked Questions
We always recommend to shut down the Shake via its rs.local/ interface (or command line), avoiding “pulling the plug” whenever possible, to not create possible corrupted files in the microSD card that would then require a re-burn. As of now, we do not have an external button/trigger switch that is able to shut down the Shake. But, with a bit of DIY, you could create something similar to what this user had done Complete RS3D station for sale. Maybe you can also contact him to ask for details. If, instead, you want to trigger it via software, this can be of help: Programmatic graceful shutdown - #2 by ivor
I think I’ve covered all your points, but If I missed anything (or you have any other questions) let me know!