Thanks for the tips about the wiper bin and the fragile nozzle! Perhaps that's why the S3D profile doesn't go to the wiper bin between every single tool change. They are using an ooze shield instead which is probably a lot more forgiving and compliant so it won't damage the nozzle.
I've done a lot more printing since then and I've noticed there are even more internal improvements than I initially realized. For example, a lot of the retraction controls, coasting, wiping, and even some of the stuff in the advanced retraction section all work properly now with the CubePro. From what I remember before, none of those settings worked properly. The automatic flow rate control also gives you a lot more freedom to use some of their dynamic cooling and speed adjustment settings.
The M108 commands and most of the other M-commands are all added internally by the software. In fact, there is even a new firmware configuration specifically for the BFB printers that defines a lot of these commands, so that's new too.
The post-processing section is definitely smaller now since so much more is handled inside the software and my exports are about 25% faster now
In fact, I noticed that the majority of the stuff in the post-processing section is just removing and modifying some of the tags for the CubePro, but the CubeX and some of the other BFB machines actually need to be able to modify these options since they use different syntax. So it was probably a very smart decision to keep some of those things easily editable in the post-processing section since some BFB files will need some slight changes. That lets them support more types of BFB firmwares.