So in this case you want to use the SYSTEM_DEFAULTWORKINGDIRECTORY env var as per your command?
In this case ZAP (and the AF) will not even get to see it - it will have been handled (or not, as the case may be) before ZAP gets invoked.
I think the problem you are seeing it just related to the commandline and not ZAP.
You can test it by trying commands like:
- docker run --rm -t owasp/zap2docker-stable
echo "$($Env:SYSTEM_DEFAULTWORKINGDIRECTORY)"
If you work out the right incantation to get the standard "echo" command to print out the right value then you can use the same format in your ZAP invocation.
Cheers,
Simon