What is "system path"? Every tool inherits the caller's path. I don't think this could be a problem unless a tool talked directly to systemd to execute itself.
in the context of "some tool that expects $0 in the system path..." - i do not understand either.
if a tool looks up a command name "x" given to it, it just takes $PATH and goes through it. the same $PATH as in your shell when you call "x" directly.
thinking more about it, you must thought something like putting "@daily mycommand ..." in crontab, then being annoyed by it not finding your command.
then the problem is not that some tools expecting a "system path", but that some tools being defiant and overrides inherited path on their own accord. which is totally unneccessary: environment is called environment because it is prepared for you (the given program) to run in.