You can continue in the initial thread normally, it makes it easier for everyone, thanks for considering in the future :o) (It keeps all information in one thread and limits the amount of threads) But do as you like of course.
As you mentioned that you are relatively new to Ae some thoughts about the whole workflow.
The first thing that I notice is that you save the RGB file and then the Multi-pass. I always would go with the Multi-pass only, to keep things more simple. In multi pass check the RGBA for that.
The “Millions+” where checked in the Quicktime (QT) settings but not the Save Alpha at all.
You can use of course QT as you like, but your settings and design indicates more a professional use. Anything 8bit/c is really not something I wish for anyone to have in terms of Quality. TV stations standard is at least 10 bit/c and that more or less based on old limitations of hardware or the cost of those. Today the minimum what I thing is acceptable for CG renderings is 16bit/c. However, I do not work in anything else than 32bit/c and linear light. Too much trouble with the limitations of anything below that.
QT is certainly a nice delivery format to clients, but it is not at all something I would use in production. In the past QT had a lot of Gamma and Color profile trouble. But that is not my point here, the most professional tip I normal can give against QT is that you write your rendering in a format that is destroyed with any problem during rendering. Power off of crash of the system is critical here. Many Compositing apps need to load the whole QT at once into the Ram to be able to work, which can disable larger projects from the start. Image sequences are the best way to go. Of course, I use nothing else than Open EXR for my work, but I’m certainly not in the majority with that in CG. It might take several years until this is a common standard. We will see. It is for sure a standard in Film Studios and VFX houses.
To get the transparency for the lower third part of your animation you need to use your Object Buffer. Place it on top in Ae the Lower third (LowerQuater_left) and use the Trackmatte Luma for it. In this way the Object Buffer will be calculated with the RGB file, and in that way the transparency comes back.
IF anything that you like to replace needs to follow your pos/rot animation, you need to set up an External Compositing Tag in C4D.
All the best
Click thumbnail to see full-size image