After doing more testing, I've decided KindleUnpack is the way to go from now on for when I run into this problem. The formatting just turns out much nicer without doing any clean up.
In Calibre under Structure Detection, I finally just entirely cleared the boxes for both "Detect chapters at" and "Insert page break before" and then Calibre's epub at least had the number on the same page with the title and text. The chapter number uses h2, and then h1 is used for the chapter title, and I'll bet that reversal is common for the books where I run into this problem.
But there are other issues that Calibre does where I'd have to tweak the stylesheet to fix, you can see in the screenshots. The chapter number is off center; the size of the first letter and its alignment is off as well. KindleUnpack doesn't have those issues.
So it's going to be KindleUnpack for me for those azw3 books that give me any issues.
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