Oh wait.. we don't really use Intune yet but I've worked with it a bit and done a few deployments for other environments already. And of course for Intune, you have to wrap your deployment package into a single Intune compressed file format. And there's your single compressed file so this is not an issue for Intune-managed clients! The "large number of files and folders issue" is really a MECM observation/mild annoyance since we're were so used to v3 being so small/fast in comparison.
I'd still be interested in hearing any thoughts/tips/advice for us MECM (and similar) deployers, if applicable, else not to worry.