Blackmagic does not currently support scaling frames from After Effects or Premiere Pro that do not directly match one of the card's supported frame formats. For example, Blackmagic cards support standard frame sizes such as 720p59.94 or 1080p24, or up to 2K or 4K depending on the card, but it wouldn't support an arbitrary comp size and frame rate like 999x999 @ 99fps.
Automatic scaling is a feature of Mercury Transmit (which is different from the Mercury Playback Engine, which is not in After Effects), which other video devices do support. When After Effects sends a frame that the video device doesn't support, the video device has the option of asking After Effects to scale the frame to a supported format. Blackmagic does not do this.
We are discussing this issue with Blackmagic. They will need to update their plug-in for Mercury Transmit to support this feature.