Yes, you can place stuff outside the workspace, and I've done that. It feels like you're fighting the system. And the fact of the Workspace's existence still means that it adds pointless workflow machinations and cognitive load to Eclipse users for no benefit, at least to those who aren't building (nearly obligatory) multi-project workspaces for Java software. The very existence of the Workspace has helped reinforce that useful, trivial actions such as command line invocations don't even make sense to Eclipse:
Read through "platform options" and the intent becomes clear: you're starting a black box, not wielding a tool.
This is all really unfortunate, since Eclipse became home to the first (to my knowledge) open-source platform for a wide range of AST-aware language tools, and all the power those can enable. These often grew up with alternative language implementations on the JVM. Other extensible development editors are still largely stuck with some flavor of regexp soup and/or a cobbled-together pot of external tools with widely varying performance, usability, and UI.
This is all really unfortunate, since Eclipse became home to the first (to my knowledge) open-source platform for a wide range of AST-aware language tools, and all the power those can enable. These often grew up with alternative language implementations on the JVM. Other extensible development editors are still largely stuck with some flavor of regexp soup and/or a cobbled-together pot of external tools with widely varying performance, usability, and UI.