Thanks for your inputs, guys. They were helpful and I think my problem is solved
@Jim: In the screen I attached to my first post I checked "Save in file tags (when possible)". However, I found out, MC only writes the Xiklone tag when I select right click / Library Tools / Update Tags from library. After I do that, the Xiklone tag shows up in MP3Tag just fine. Before I do that the Xiklone tag seems to be stored only in the library. Or am I missing something here? Is there another option that needs to be set for the tags to be written to the files automatically.
@Brian: Nothing fundamentally wrong with MC's transcoding. I simply find it somewhat limiting, as I cannot easily chose the tool to be used. I like SOX for resampling, qaac / Apple Core Audio for aac conversion and DSDMaster for DSD to PCM conversions. Xiklone gives me the freedom to use whatever I would like. That's about the only reason I have. Don't get me wrong, MC is a wonderful tool set, and I would have given up on streaming audio a long time ago without it. But like with most multipurpose tools there is usually a specific tool that one prefers for a specific task at hand. Most of the stuff I actually do in MC.
@ferday: See my answer @Jim.