I see your points, but I think you are speaking about this at a higher level that isn't necessarily specific to this particular implementation.

I agree that when used by the direct posters, affiliate links cause a misalignment of incentive because the poster isn't necessarily adding value to the community but rather to their affiliate account. This can be done very naively or be abused. Users suffer both ways.

This however isn't the case here IMO because if Reddit is auto tagging all links the posters are pretty much in the same boat that they were of Reddit hadn't tagged those links.

You could say that because this is a revenue channel for Reddit they'd optimize tagged posts over non tagged ones when promoting content. That however mostly gets resolved by the same logic as above, plus we all know how stuff gets to the top of Reddit...

Lastly, communities making some revenue is, again, not a misalignment. Using the same logic as above, all auto tagged links are again just links. Hence, a community that generates good content would get some revenue. It's pretty straight forward in my opinion.

Lastly, most affiliates pay commission on sales and not impressions (and if they do it's really tiny). So the context and the targeting are the most important pieces.