Can I Plan to Write a Scholarly Book in LuaTeX or ConTeXt This is a general question only. By now I am only a graduate student, and you might laugh at me for this, but maybe some day I will publish a book. I am considering to use LuaTeX or ConTeXt, but I am afraid most (if not all) publishers cannot read them. Does the writer necessarily has to sent the publisher his or her work in the format publisher can open? 

I know most journal publishers accpet LaTeX only for article submission. But what about books? Imagining the book is completed, reasonably proofed, and has accordingly compiled a PDF, and the writer sends the PDF to the publisher. I assume the book is of some value, of course. But the source is written in LuaTeX, or ConTeXt, or some rare format. 

Will it still be unreasonable that the writer collaborate with the publisher in a format only the writer can open? Or even if he or she uses a format the publisher cannot read, is it possibly viable that he send a PDF file only, that the publisher suggest corrections and advices on format, and repeat the process, allowing the writer to make change?

If a certain format is almost universally rejected, I will think twice in what format should I write my miscellaneous notes, thoughts and sketches related to my field, since it is hard to tell whether in the distant future I will organize material into a book.

Supposing not, what formats do scholarly publishers approve in general? I suppose pdflatex-compilable LaTeX files is almost universally acknowledged, but are there other options? Some say that a small percentage of publishers also accept Microsoft Word, and I am aware that, but I hate Word, sorry.
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.)