Noted! IMHO it’s a pity that the goal isn’t a little more ambitious, but I don’t have to implement a solution so I’m ignorant of the issues. 
Maybe escaping to raw HTML is a workable solution. For this book I only have two little tables and I’m going to use the hack at How to get tab stops into epub - #12 by ds.
Without trying to sound like a know it all (and probably failing!), it seems to me using Markdown as an intermediate compilation language (which is how I understand the statement “the compiler uses Markdown to create the HTML”) is not the best solution. Translating from a more expressive language like the editor’s to a less expressive language like HTML is always going to present problems, but going via a language that is even less expressive than HTML–Markdown–only increases the problems. Why not just generate HTML directly? There’s no rocket science in that.
Just curious–and sorry to be a pain in the ass!
P.S. Don’t get me wrong: I love Scriviner! The editor and “binder” environment is really well done. The way through the compilation process is pretty well done. And the PDF output is good enough for the purpose of my little book.
P.P.S. If the editor representation is RTF then maybe a tool that goes directly from RTF to HTML could work. Five minutes searching found this: GitHub - lvu/rtf2html: RTF to HTML converter for use both with your applications and as a standalone tool. Small and fast. Processes tables better than any other tool I've seen..