It is not possible to call such things from the command line. CC3+ wasn't written with batch processing in mind.

You can talk to CC3+ from an external program using the Intercom interface however, which means you can send commands from an external program which are then run as commands inside CC3+. I don't have a tutorial for that on hand. Some information can be found in this old blog by @saunderl http://cc3-developer.blogspot.com/search/label/Intercom

The second alternative is to make your own XP which opens up a lot of possibilities for expanding CC3+ with your own code. I don't think you'll be able to implement more command line options or prevent the gui from loading though, those things are (most probably) beyond what an XP can do.

When you need to to a precise export, make sure that you only export the map itself, and not any border/screen, as this will mess up your calculation. This is typically what causes the drifting you describe since then borders steal some of the pixels you calculated for the grid cells, they suddenly aren't 50 pixels anymore. Use the save as rectangular section to accomplish saving just the map. Make sure that the export size is calculated correctly, for example, a 11 by 12 squares map sghould be exported as 550 by 600 pixels to fit with 50px/square

Also note that 50 px/square does not give you a very high quality result if you like to zoom in as in your image above. I recommend at least 100px/square, MapTools handles that fine (Of course, that also means that the players get sent a bigger file, so you need to weight quality against bandwidth/transfer times here)

Generally, I also prefer to leave the grid off from my CC3+ export, as it generally isn't needed. That also minimizes the effect of drift a bit, but again, drift won't be an issue if the export size is correct.

Maybe my blog article here can also help you a bit:

Not sure why the tools are identical. Might be just to allow for different filters to match, i.e bot Terrain ad Vegetation.

I don't think any belongs on a different sheet. both are background polygons, and there are no other sheet where they would fit in as far as I can see. I thought about the vegetation sheet, but then they would end up overlapping things in a weird manner, so I don't think so.

Correct.

You could edit the template behind the maps instead, that would affect all future maps made from that template, but not existing maps.

Seems to be an error with the .symfill files themselves. I've alerted the appropriate individuals.