Hi Joe,
First, once a survey is published, it will be hidden if you are logged in as a user that is not the publisher, so that can provide some organization.
Secondly, there are a couple of geeky workarounds you could do with a bit of effort. All survey designs in Survey123 Connect are stored in "<user home>\ArcGIS\My Survey Designs"; you could create multiple folders to store the different projects and then switch the name appropriately (this works a bit better on a Mac because it supports Unix-style linking). You could also do the same by enabling git or another version control system and creating a branch for each customer.
Regardless, I've written down an enhancement issue to look into this. You mention that you have surveys across multiple agencies- would you have advice/suggestions for how this should be done?