Can I Plan to Write a Scholarly Book in LuaTeX or ConTeXt
It's possible that you could find a small or specialized publisher that is happy with an unusual format, but I don't think most academic publishers would be able to work with LuaTeX or ConTeXt.  It just won't be part of their standard workflow.

It's very unlikely that they will let you control the file and make all the changes yourself.  Instead, publishers almost always edit the file themselves, since that's more efficient and gives them more control.  If you care about doing all the edits yourself, you should mention it early and expect to be turned down by most publishers for this reason alone.

In practice, I don't think the editor will even think about the format issue if you don't bring it up.  They'll assume you are using LaTeX, and they'll be surprised to learn otherwise when it's time to submit your manuscript for copyediting and formatting.  At that point, they aren't likely to reject it for format reasons, but they'll probably do things that make you unhappy.  They might try to convert it to LaTeX themselves, or even retype everything from scratch.  Any fine details of formatting will have to be reconstructed, and the chances of getting everything exactly the way it was are slim.  If you have strong opinions about formatting, you should try hard to avoid this outcome.  (It's better to convert it to LaTeX yourself than to have them do it.)