If you’re interested in an approach that bypassing any front end syntax via Markdown parsing, and basically just treat Scrivener like a pure plain-text editor for writing LaTeX, check out this thread, and the example project template I’ve been working on.
The HTML comment method for inserting LaTeX through MMD will no longer work with the next version of Scrivener. We’re upgrading the core engine to MMD6 and so the method I described above will be better if you’re starting a new project right now.
Here is another post on the general approaches Scrivener provides.
Yeah you can stash your boilerplates into the compiler with the “custom” setting, but if you’ve already got that all set up in your texmf folder or wherever, just getting the content out with “none” is good.