If you aren't doing it already, remember that relative coordinates are your friend when pasting with regular intervals. Since the next paste is relative to the previous one, one can mass paste by using the exact same relative coordinates multiple times in a row.

Not directly. I recommend drawing around the settlements with the tool, then placing individual trees after that along the edges to give a tighter fit (And finish off with a sort symbols in map to arrange them properly.)

There is also the exclusion commands, this allows you to specify areas to exclude, but this only work with polygons, not symbols.

There is a bug with a few of the Cos3 templates. You can grab an updated version of the installer from your reg page, or download the fixed templates only from here. That should hopefully fix things for you (note that fixed templates means it will work properly on new maps crated from these. For existing maps, I recommend just copying things over to a new map once you have confirmed this fix works for you)

Your map is 250 by 200 feet, so that is 50 by 40 squares. Each square in FG is 50 pixels by default, so should be 2500 by 2000 pixel export if my calculations are right

First, load and apply the Mars color setting

Then, go to the Altitude tab of the Lighting and Color dialog, here you can set blue colors for the sea. Just set the sea level and lowest depth color, FT3 will calculate those in between, and you'll probably want to bump up the value for number of colors too.