Based on what we saw with the 10th gen Civics I would say it heavily depends on your local dealer. Some care, others do not. There are numerous verified reports of warranty work being completed on tuned Civics.
I would take what Honda reports and throw it out the window. Instead look at test data from independent sources like Derek Robinson and John Vega. They have both tested both 10th and 11th gen Civics on their dynos and the results were unfortunately not favorable at all for the 11th gen models...
It's going to include everything associated with the shifter end of things. You may want to consider the linkage bushings, but you've already taken a huge step with the shifter itself. Have fun!
If it's not supported, you will need to work with them to get it supported. I am sure they will be happy to help, as the 2020 Canadian Si is sure to be a popular model to tune.