I have some (but not all) of the answers for you. In the V1 store they are currently selling two boards, the Jackpot and the SKR Pro. The Jackpot runs FluidNC which is an implementation of GRBL. The SKR Pro runs Marlin which is the firmware on a majority of 3D printers.
If I can load existing files, will I get the same results or will things be different with the different controllers?
You need to generate new g-code for a specific firmware (Marlin or GRBL). The piece of the CAM (VCarve) that makes that translation is called a postprocessor. VCarve has a postprocessor for GRBL, and you will find a custom Marlin one referenced on this page. In VCarve, you will have to select the appropriate postprocessor for your control board and re-generate the g-code for that controller.
looks like the designs are loaded and run by SD card
There are multiple methods for delivering g-code to each of these two boards. On the Jackpot (which I’m not using at the moment), it appears that the preferred method is to send the files wirelessly to the SD card and initiate the job from the wireless interface. You can pause the job from the wireless interface even though you are running the job from the SD card.
On the SKR Pro/Marlin side, files on the SD card can be run from the display in TFT mode, run from the display in Marlin mode, or delivered to the card over the USB cable using g-code sender software. The V1 documented g-code sender is Repetier-Host. To communicate wirelessly with the SKR Pro requires additional hardware. Note that pausing with Marlin is problematic. Pauses go into the queue like other commands and can take a while to move to the front of the queue. There is an emergency stop feature that can be enabled in Marlin, but the job cannot be resumed from this kind of stop. For either board, it is good to have a way of killing all power to your machine (hardware emergency stop of some sort).
Is it possible to connect basically a joystick to do gross setup movements, or is it only possible to use the touchscreen?
On the SKR Pro/Marline solution, there is an interface that can be used for hooking up a physical joystick. You will find this very long topic on the how to implement the physical joystick here. Marlin also allows multiple serial inputs. People have built pendants for their machines using this interface. This design inspired me to build my own pendant.
Personally, only a small percent of my jobs requires a high degree of squareness, so most of the time I physically/manually position my router (X, Y, and Z) before I turn on the electronics. The position when the control board is booted becomes the origin for the job. Unlike a 3D printer, most CNC jobs are defined relative to the stock, not the working area.