Ok, that was a big problem I had/have and how I dealt with it. I have an hourglass image that I like to have above the roman numeral chapter title, but I could not get the toc to work. So i HAD to have the roman numeral first, but I did not want that. This is what I figued out. Not sure if it is the most elagent way, but it works. In InDesign I made a paragraph style for the roman numerals and put the color as white so you could not see it. Then I type the roman numerals at the top of the page when a chapter started and, like normal, used that paragraph style in the toc. You can stop there if you want, but I didn’t want people to see 2 sets of the chapter number if they read in black/white or sepia.
So, what I did was output the epub, crack it open, and remove the first set of chapter number text at the beginning of each chapter. (The toc will still work.) Then I reassemble it and make it a mobi. It is kind of a pain having to remove the chapter titles in each file, but you get used to way to looks in the cracked open epub and you can quickly find it.
I suppose you do not need to make the text white if you are just going to remove it, but if you miss one, you don’t have to worry it will look weird, unless the trade reader is using sepia our B&W.
Works pretty well as a work around. Hope that helps.