The video port coming out of the Raspberry Pi SoC is HDMI, hence the choice of the connector. We've put the connector on the top of all of our products to lessen the chances of the cable accidentally coming lose. The top and bottom of the case is primarily used for vents. We'd have to make them smaller to fit a VGA or DVI connector there and that might negatively impact heat dissipation. That said, I agree that HDMI is not as rugged. A particular problem we've encountered are cheap cables which connect the shield to ground.
As for flashing the products, there's a micro USB port on the front plate which allows flashing the eMMC from an attached laptop or PC. It's also possible to mount the eMMC to retrieve logfiles from the machine that way. When the machine is booted, it senses whether bus power is provided on the micro USB port. If so, the USB port on the Raspberry Pi SoC is switched to gadget mode instead of host mode. You then need to run a little program called rpiboot on the attached laptop which downloads a firmware to the Raspberry Pi to turn it into a USB Mass Storage Device. Afterwards the eMMC pops up on the attached laptop as an external drive:
https://www.raspberrypi.org/documentation/hardware/computemo...
It would in principle be possible to build small gadgets which users plug into the micro USB port and which automatically flash the attached Raspberry Pi without the need for a laptop.
Another possibility would be to split the eMMC into multiple partitions, one containing the regular OS and the other to store an update image. The system would initially boot into a RAM disk, determine whether an update image is present, extract that over the regular OS partition and reboot. The update image could be deployed via ssh.