Can you add a standalone mode like in visualGDB ? http://visualgdb.com/tutorials/arm/standalone/
It will be helpful to work on system libraries, to have a separate builds with access to the core libs, without affecting other projects.
You can clone existing development platform located in ~/.platformio/platforms/, open platform.json and change name field (for example, add -modified suffix). Later, you can use different development platforms. See
For example,
[env:original_dev_platform]
platform = atmelavr
[env:modified_dev_platform]
platform = atmelavr-edited