Set working directory in `VBoxManage guestcontrol run`
Solution 1:
If your guest is Windows, try using CMD.EXE and START, something like
VBoxManage guestcontrol "Windows 10" \
run \
--username "john" \
--exe "C:\\windows\\system32\\cmd.exe" \
-- cmd.exe /C "START /D Z:\\path\\to Z:\\path\\to\\bin.exe"
should suffice. You may need to modify it to suit your needs.
CMD.EXE supports /C to run given command and terminate, in which we run START.
START supports /D to run a command in a specified directory, in this case we're using Z:\path\to.