Preventing Table of Contents Generation

Is there a way to configure Scrivener so that it won’t generate a Table of Contents on compilation to mobi or epub?

No, this is automatically done during the compile process. We do have plans to allow more customisation for this, but until then you’ll need to compile to the .epub format and then do some post-processing to edit or remove the TOC. We recommend Sigil as a free, easy-to-use ePUB editor. From there, you can take your edited .epub and open it in Amazon’s Kindle Previewer to automatically create a .mobi copy using kindlegen.