Best practices are of course a bit dependent on content, but in seeing a lot of documents I can say that most users opt for the easiest (and most Flash-like!) route of adding items to a top-level group and setting that to scale proportionately and use Zoom Contents to scale everything inside (css transform:scale() under the hood). The main downside to how Flexible Layout is implemented is that users have to do this for every scene in Hype. There is some older code that does the equivalent for the entire document and can be added to the HTML head:
I'm not sure all you're planning, but this could be injected at export time by Hype or when going into Blocs.