Hi Klemen,
You can fix this issue by selecting the correct platform and I/O interface extension in steps 1.1 and 1.2 of the HDL Workflow Advisor. In particular, the IO334 module by itself does not have any digital I/O channels, and requires an IO3xx-21 or IO3xx-22 extension module to map additional TTL channels.
As to the warning messages, they will always be displayed in the HDL Workflow Advisor if you change the platform in steps 1.1 and/or 1.2 and make previously mapped interfaces unavailable. These warning disappear as soon as the input/output ports of your model are re-mapped to new interfaces.
Finally, the error message "Incorrect model configuration settings for HDL code generation" is expected in your case, and is explained in the following MATLAB Answers post. I hope this is helpful!
Dimitri