Microsoft stated that bringing ChakraCore to OS X and Linux will allow developers to build cross-platform applications. However, seeing that the engine was originally developed for Windows, it will obviously have a few Windows dependencies, but the company is working to improve on that, with backward compatibility being a major focus as well.
About Node-ChakraCore on Linux, Microsoft had the following to say:
Earlier this year, shortly after open sourcing ChakraCore, we submitted a pull request to Node.js mainline to enable Node.js to work with ChakraCore. Today, we are taking another major step in the Node-ChakraCore journey. As part of enabling Linux support for ChakraCore, we are also sharing the first preview for Node-ChakraCore on Linux at our repo. This is a very early step in our full support for Linux, but we are excited to share the progress.