Re: workflow

With the Aja cards, you have the option to either in RGB 16-235 colorspace in AE in case you want to render into a Media 100 codec, or into 0-255 if you want to render into an Apple codec like ProRes. We use ProRes heavily these days, so most of the time we are monitoring the full range 0-255 signal in AE, which is what you are seeing with the Blackmagic card, I guess.
You could either render into ProRes or another full range codec, which would give you the same image in AE and Media 100. Or you could apply a Levels filter on an adjustment layer in AE on top of your composition before rendering, with the output white set to 235 and the output black set to 16. Turn it off for working and monitoring in AE, and turn it on for rendering. This way you should get correct renders from AE into Media 100 codecs.