I think the Calyx is definitely the superior DAC. They both share a warm, rich, organic type of sound that many will find "musical" but the Calyx is more dynamic, brings lots of the inner detail that the Havana lacks, throws a HUGE soundstage with large images, is more airy in the highs, and has better defined, more authoritative bass. The Havana still has a very wide and fairly deep soundstage, but smaller in scale and a more recessed presentation, and maybe carries a tad more texture and richer tone in the mids. I think it also has more leading edge/transient snap. The Calyx is a somewhat soft sounding DAC in that sense, but only in that sense -- the transparency and dynamics are very good.
My general feeling is that in largish rooms, for big scale with big, highly resolving sound and complex music, the Calyx does a great job and the Havana is insufficient. For small rooms and more intimate feel and smaller ensemble music the Havana is very engaging and eminently musical. Used in my bedroom system, I enjoyed it a lot and its shortcomings did not draw my attention at all. Unfortunately I now need a DAC with volume control in both systems as I'm moving from an integrated to a power amp in my bedroom and probably a preamp with no remote in my living room. As mentioned in the original post, I also feel the scale is a little TOO large with the Calyx and my new Tannoy Turnberry SE's.
If you read the Stereophile review of the Weiss DAC202, that is the sense I get about the Calyx, so I now understand why people describe similarities between the two. I am now using a Bel Canto DAC3, and I also agree with the comments about the sonic signature of the DAC3.5VB in that review. It all depends on taste.