Fixed by updating the .hgsub files to make sub-repositories relative.
e.g. for SoQt:
data = ../soanydata
src/Inventor/Qt/common = ../sogui
build/general = ../generalmsvcgeneration
This is not ideal, since any forks would require the subrepositories to be forked as well, but I couldn't find any other ways of doing this without explicitly pointing to an absolute location, including access scheme (which would break http vs. ssh access).