Scoped storage is certain a pain the a**
However, I don't personally have many issues with it as I almost always work from a laptop and connect via the WiFi IDE which includes a good remote file browser. This file browser allows me to download and upload folders and SPKs and also you can right click on SPKs to install them remotely (and maybe even APKs, can't quite remember).
I guess you guys are working directly on device then?
The new on-device file browser has a 'Import/Download' option that allows you to move APKs in and out of scoped storage...is this not working for you?
Note: There is a bug in the latest beta release which means that you have to disable password and enable auto-wifi and not touch the wifi button to make things work.
When scoped storage first 'hit us' we pondered the idea of storing the DS project folder in the root of the internal sdcard (by asking user permission or registering DS as a file manager), but thought that this would mask the concept of scoped storage from our users and they would get into no-end of trouble when trying to publish their APKs since they would not anticipate/learn the effects of scoped storage and expect to have freedom to read and write to top level folders (like in the good ol days).