Stacked nodes at path origin are removed

I'm working on a variable font where due to the design sometimes two nodes need to be stacked on each other. I've found upon exporting the variable font stacked nodes at the beginning/origin of a path are removed whereas other cases of stacked nodes are left untouched.

This is my source glyph (stacked nodes are highlighted in red):

And this is the output:

As you can see only the stacked nodes at the beginning of paths (marked with a triangle) were removed.

Is there anything I can do to remedy this? If the only solution is to move the nodes 1 unit away from each other that's fine but thought I'd see if there's another way to solve this. I thought maybe the `--keep-overlaps` would help but it didn't affect the output.