Yes, this is certainly possible. RT Box can be emulated either as a physical inverter or plant (called hardware-in-the-loop simulation) or it can be emulated as a controller (called rapid control prototyping). These definitions are described on this page.
In your case, it looks like you are interested in performing a hardware-in-the-loop simulation, with the RT Box acting as a plant, and exchanging analog and digital signals with a real MCU target.
An application example of this -- of an H-bridge Converter (emulated on the RT Box), interfaced with a real TI C2000 MCU is provided on this page. Checkout the example titled "Embedded Code Generation: H-Bridge Converter". I also attached the write-up to this post.
Please note that to run this demo model, apart from installing the RT Box Software, you also need to download and install the TI C2000 Target Support Package.
To learn more about the RT Box, please go through these tutorials here.