All lines resulting from a preprocessed template appear to correctly use system defined line endings except for those that are defined inside of a control block (<# #>).
Given a simple .tt file with all uniform line endings on Windows:

And then after running preprocess from Rider IDE, we can see in the TransformText() method that output line endings are not consistent:

This was repro'd using Rider 2021.3.3 (bundle 2021.3.238). Switching project settings to use explicit line endings did not appear to have an effect. Screenshots are from Notepad++ for easy line ending visibility, but any actual manipulations were all done inside the Rider IDE.