The color levels also aren’t the issue. It’s DSLR footage, import settings are RGB. If I select Rec709 when importing, the blacks are crushed but besides that the image looks just as bad, with heavy blocking. Transcoding via AMA is also a lot faster. Retranscoding my whole footage wasn’t really a big deal.
There seems to be another difference between import and Ama-link-transcode:

The Image shows the RGB-Parade of a black to white gradient I created in AE. As you can see, importing changes the gamma, while transcoding keeps everything as is. The gradient is RGB, thus 0-255. Why is it that the AMA-linked clip is still displayed as 16-235?