Regarding the "super-bonus map", I don't think it's such a problem. Think about it, when do you want to look at it? When you're planning strategy (large scale), you'll be zoomed out than anyway. Of course you'll be zoomed in a lot, but at that time, the "mini map" (to borrow a term from RTS games) doesn't matter anyway.
Of course, it would be really sweet if we could get Fizzer to implement a (floating) window that actually implements a minimap; an actual minimap by default, but which map-makers can override with something else if they wish. </I can dream ;)>
Warlight uses a very simple algorithm to determine "center" of a polygon - it just takes the center of its bounding box - and as you can see already, this can produce "unnatural" results, for example on Spain or Croatia.
I can think of three possibilities which might/could work:
Make a (gray) outline of the countries, with a normal bonus square in it. Doesn't look as good, but does work.
Determine where you want to bonus number to appear. Make a square, centred around that point and big enough to cover the whole country. Make this the bonus area. Then, draw a "negative" of the country on top of that, to "cut" the square into the correct shape. Careful, I'm not sure whether this will work! (It definitely would NOT work for territories, since Z-order is ignored by WL, but I have no idea what rules apply for bonuses.)
Ask Fizzer to allow (optionally) determining centre points for bonus polygons.
The easiest way would be to compose each bonus shape of two parts; the outline of the country (which ??somehow?? gets the correct colour) but which doesn't show the bonus value, and a (manually positionable) square which follows the normal bonus-square rules. Unfortunately I have no idea how to make that outline... :(