Can't place a marker on the map

[?]

That is very weird and uncomfortable

How to fix that?

[overdev]

it was fixed on the SE version.
as far as I know it requires the flat map marker mod, which is used in Enderal for the map, that the coordiantes for it is centered at X = 0 and Y = 0 and I think you would need to do some additional stuff, I'm not really sure how cause I didn't work on it.

You could ask on the Enderal SE discord server how exactly they did it: https://discord.gg/s9H925auNN

But in general I think thats not worth it cause the mouse needs to be pretty far away from the normal markers in order to place a custom one. a few centimeters / 1.5 inces on a 23" monitor (hard to describe).

Custom markers only makes sense if no other markers are near the location you want to set one.