Placing custom files under <matlabroot> is generally not recommended. Up until R2019a, we did not check the location of custom target .tlc files, so they would work fine even if they were located somewhere under <matlabroot>.
However, in R2019b, we introduced the new Simulink Toolstrip. And it was decided that when launching the "Run on custom hardware" app, it checks the location of the .tlc file specified in the model configuration. If the .tlc file is under <matlabroot>, then only certain MathWorks provided targets are supported, but not custom targets. This is why the app prompts you to switch the target back to grt.tlc.
To work around the issue, place your custom .tlc in a different directory outside of <matlabroot>, and place the directory on your MATLAB path using addpath().
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