You need to click the Collapse Transformations checkbox on the Precomp layer. Just be aware that this may have other implications, especially if you are using 3D layers and cameras in one or both of the compositions.
Yeah, almost every layer is 3d with camera moves. I guess I could just go and key out the black, but I do wish there was a way to keep the transfer mode
and one of those comps involves setting the transfer mode of some layers to add, in order to get rid of the black background.
Well, no offense, but that's a rubbish workflow. If you need genuine transparency, then create it properly. It's as simple as that. Use Shift Channels, the Channel Combiner or any other effects to "unmultiply" your layers or rewire channels. Doesn't even matter whether you do it on your source layers or the combined result of your additively blended layers - whichever works best to give the desired look.