Yup, I did some more testing over the last couple days, and even without my customizations (those are in a sub-theme anyways) and a fresh install of just the Darkness theme, importing the CMS' xml file always has the same result.
Also, I just checked my template notifications and the only warnings I get on the site are for the outdated (and untouched since upgrading) 4.1.4 styles.
I ended up exporting my own customized version and importing it to a new sub-style of a fresh install of Darkness without the CMS merged into it.
Have you been able to duplicate this? If it helps, the order I tested was a fresh Darkness install, then merging in the blog's xml file, and then merged in the cms' xml file. I managed to get the weird template thing to happen four times when I tried this.
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