If I want to "mass load" the base with sand, should I increase the overall volume correspondingly?
Yes, you must increase internal cabinet to accommodate for anything that you put in there. Bracing, sound absorption material, sand, everything. When building speakers from scratch one of the most common things people do is forget to account for the volume of the speaker itself.
The drivers are rear mounted. Therefore the hole I cut for the driver on the front panel should have a radius on it and not a square edge, for diffraction reasons, right?
You can route the corner down a bit if you wish but it is not critical.
Cabinet "tuning". I know this is a function of port area / depth. What if I want to use a commercially available port with a flare on it? I've read that's a better way to port. Anyone know somewhere I can learn more about this? I'm port-illiterate.
Port lengths are calculated differently for straight ports and flared ports. So make sure if you decide to go with flared ports you recalculate the port size and length. I use flared ports, but honestly only because I find them easier to mount and secure. I have never noticed an appreciable difference in sound.
And lastly, does the box volume have to be dead-on? Of course I'm thinking of building it a bit bigger and then I just add solid wood inside to reduce the size if need be.
No the volume does not have to be "dead on". Of course you want it as close as possible though. And your plan is a good one. For sealed or ported designs I build .5 liter too big and then deaden with sand to bring the volume back down to specs. Then I experiment with polyfil, sand, and wood blocks to adjust the volume to get the sound to my liking.