For PDFs, we use Syncro Soft's PDF Chemistry. It provides CSS-based configuration of PDF output. We find it easy to customize PDFs exactly how we want them. It is included "for free" with Oxygen, although a separate license is needed for command-line (script-driven) publishing.
For HTML5/online help, we are still trying to figure things out.
On the CMS front, Oxygen has an excellent Git add-on that integrates Git client functionality directly into the Oxygen environment. I can't say enough positive things about the Git add-on. You can push and pull commits, switch between branches, perform conflict resolution, explore commit and blame histories, and even stash/unstash changes, all directly from within Oxygen. Conflict resolution can be performed graphically using Oxygen's excellent WYSIWYG file comparison ("diff") tool.
Good luck on your journey, and welcome back to DITA! Things have advanced quite a bit in the last few years.