There shouldn’t be a need to change account names or folder structures. Consider using symlinks to create an alternate path to your user folder. For example, on the laptop a symlink in /Users that uses the home machine’s account name to redirect to the laptop account name. Scrivener looks for /Users/homemachine/Dropbox/MySyncFolder and is silently redirected through /Users/laptopaccount/Dropbox/MySyncFolder. I used that technique myself for years, back when I had mismatching account names since so many Mac programs are simply not coded to work with UNIX shorthands. I’ve added a note to look into the tilde thing though—relative links in general are something we’re looking to support better in the future, while this isn’t strictly speaking a relative link, it fits in with that goal and would be a whole lot easier than having to explain to people how to make a symlink. 
Regarding “Moom”, I’m not sure if this is the same thing, but have you checked out Scrivener’s own layouts feature? It’s in the Window/Layouts/Manage Layouts… menu. It will not only save split positions (and existence), but all manner of settings if you wish. Just about everything you can do to a project window will be saved, even outliner columns and whether or not the secondary split has a header or footer bar, if the Binder is showing, etc. I have one that removes all UI elements and maximises the window, mainly I use it for freeform corkboards.
You can already establish links from your Binder to files on the drive (see File/Import/Research Files as Aliases—or just drag in your own aliases bulk, the alias itself will be archived just like normal files, but will also display content in the editor pane if the file type is one that can be). Granted that won’t accept links to text files to reduce confusion—but with text you already can expose the content to automation with the folder sync feature.
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That’s not really a Markdown thing though, right? If I understand you correctly you’re just talking about the default font settings for new documents in the software.
You may also be interested in this forum thread, which has some example settings you can apply to Scrivener which will make the main text editor look and act more like a plain-text editor. (Note you might want to save your existing preferences to a preset before trying them—there isn’t anything in them you couldn’t emulate in your settings of course). It’s also worth noting that the user interface is very customisable. You do not have to stare at font controls at the top of your editor if you don’t want to.
There are no plans to add syntax highlighting to the software. This concept is not compatible with how the text engine works. If you want a more thorough explanation there are threads in the forum where this has been discussed.
One comment I had though: you are aware that Scrivener can generate heading codes for you, right? It can calculate the number of hash marks based on its outline depth and print the title of the document between them. This is all done in the Formatting compile pane—of course you can just type in headings wherever you want in the editor, but I rarely ever do that with Scrivener. It’s one of the few forms of Markdown it can actually generate.