Hi Jason,
The actual answer is probably "it depends". The most common workflow is to use SImulink + MBDT or algorithm development and upfront testing on a real processor. However, the code generated using Simulink and MBDT is very good in quality and performance - it can be used for production.
In your case, I think you would use what we call Algorithm Export: you would use SImulink + MBDT for algorithm development and testing, and as you got closer to production, you would only generate code for your algorithm and import that into MCUXpresso for integration and deployment. Simulink is great for algorithm exploration and simulation, but it's probably not the ideal tool for the bootloader integration you mention. My take is that you probably should utilize a hybrid approach - that way you can leverage the various tools and packages where they are strongest.
HTH,
-Brian