Yes, the converted dual-ISO shots will look qualitatively the same as normal shots taken at the same exposure settings (at the lower ISO). However, the difference is there when you manipulate the photo in post (e.g., Darktable). For example, if you increase the exposure, you should see noticeably less noise in the shadows. This gives you more post-processing latitude, including if you want to apply crazy "HDR" effects.
For Linux, you can build a native version of
cr2hdr from the source code, but if running it through Wine works for you, there should be no difference in the output. Note that you should probably use the 20-bit version (
cr2hdr-20bit.exe), which has a bunch of improvements.