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Yeah, you're probably not going to be able to include your own MathJax script (local or remote) with its own config. Sigil's Preview automatically injects the script tags with its own version of MathJax (and its own local config) behind the scenes whenever MathMl tags are encountered.
The build-time is definitely my fault. Since only two lines of one file were changed, I didn't do a full compile from scratch. It probably should have occurred to me that that might happen, but it didn't.
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