The thing is: if you are not creating a project with the correct tool chain, nature and plugins referenced, you won't be able to see the toolchain (optimization, etc) options.
How do you think the IDE will know about the compiler optimizations, if the project is not configured correctly for the compiler/toolchain you want to use?
So: you have to create a proper/correct project if you want to use all this.
if you create just a 'project without any toolchain and no SDK information' you won't be able to use this all.
If you don't want to use the SDK, but just use a 'bare toolchain' project, then I recommend you install and use the GNU MCU Eclipse plugins.