After some experimentation, I've identified a few issues with Kinja-served affiliate ads and would like to report them, plus give a heads-up to anyone else who may be interested by doing it with a public post.
First of all, the major affiliate marketing networking firms all tack a 1x1 counter image onto the back of their links, both text and banner ads. For some reason, even though these images appear to be true-sized, Kinja is either making them larger or putting them in a box because every place you put an ad, you also get a big blank square on the draft display.
There also appears to be a display problem with a straight Amazon image ad. The picture comes out very large, but that could be the image's true size. The real problem is that Skimlinks sees the image ad and converts it to Kinja's Amazon affiliate code, leaving mine out. (This does not a seem to be a problem with banner ads from other programs. From my attempt, it appears to be limited to Amazon, but I didn't try every network or every program)
Skimlinks also takes Amazon text ads and redefines them to count for Kinja. Though again, it appears to leave text ads from the other networks alone.
The closest that I can get to a properly displayed and coded, product-specific Amazon affiliate ad at this time is their iframe, like the ones often used by the Gawker blogs. Though no matter how I enter the ad, Kinja leaves off the "buy now" button (on the draft display) and that may be a violation of Amazon's terms, but because it doesn't come with a counter image, there's not a big improperly sized box and Skimlinks appears to leave the link coding alone. There's just not a "buy now" or a bottom border, if you try using Amazon's bordered display.
I thought this all should be reported, so at least Tech will know. Also, it should probably be noted for anyone interested in using Kinja-served affiliate ads that there may be some contractual hurdles, especially with the non-Amazon networks, but that's probably not Gawker's concern and they're not related to Tech.
Right now I'm leaving my experimentation page in draft mode, but if I need to open it up, if I can help clarify any of the issues or if I can be of any help, I'd be happy to respond.
(Please note that I've purposefully not shared this with a community forum)