You can now post on-the-fly redirect links on affiliate URLs. More info on the edit pricing/delivery page right by the landing page URLs. You have your affiliate link, w/sub id optionally, and at the end you would specify the redirect URL. When the link is clicked, it would go to that URL instead of your default URL. 

Can I have an alternate custom tag that would go on the end, in the form of a variable, just like the redirect URL? 

Append &affiliate_custom_1=YOURTAG to the end and put a zero in the normal slot for the tag.  It should work.