I left constructive criticismyeah man, you're totally reasonable and non- aggressive and only want to help...
obvious troll is obviousAnyways, on to something that I actually care about:
So you say your bonuses overlap in warlight, but you see no problem in inkscape. That's because, while you can set the stroke width in inkscape to whatever you want, it is always changed to a width of 1 in warlight.(for territories, that is)
So if you want to not have overlapping territories, follow these steps:
Let's say you got a bonus you want to make. You have drawn the line separating it from the rest of the map.
(1) Select the line and set the stroke width to 0.8
https://prnt.sc/gv6dum(2) Change from stroke to path (ctrl + alt + c). It should look like this:
https://prnt.sc/gv6f40(3) Select the line and the map and break apart (ctrl + shift + K)
(4) Draw the individual territories inside the bonus and do a division (ctrl + /) It should look like this at the end:
https://prnt.sc/gv6idg