No, the map is not used to measure heights/depths. This info comes from the BDI/BFD file (it's a huge 1GB file
). The actual (visual) maps (the .RAW files) used in the map/plot screen can be changed without affecting sea depth and land height afaik though I have not tested it in game. I tested it with the mission editor... I think even altering the RAW-map (land outlines) has no effect whatsoever in game, and things like new land or rivers/channels must also be added to the BFD file.