This last render looks very good! 
About the grouping/parenting issue, collections are not groups, and parenting has its own quirks; but if you create a collection for the light for example, you can just add instances of that collection via Shift+A/Collection Instance instead of duplicating it, and the instances are handled as a single object, with the advantage of receiving any change you make to the original collection. So if you change the light intensity or the glass thickness, every other copy will have the same change too.
Another way around it is to parent objects to Empties, so the empties represent groups, there’s some addons that can help with that:
GitHub - machin3io/MACHIN3tools: MACHIN3tools is a free, continuously evolving collection of blender tools and pie menus in a single customizable package.
About the branches, don’t know any tutorials that go into detail about this specific thing, but since you need just a section of the tree you could just model a single branch and use a hair particle system to create the little pine needles, those could be just textured planes.