Gosh... You bring up a lot of good questions. I really don't know the answer, so I hope others will help you.
One item that you could do in the meantime is treat the magazine as if it is a series (which they really are) and number each issue sequentially. That might make them appear as independent titles.
You might also simplify your question a bit and ask it over at the Calibre forum. I don't subscribe to Amazon's periodicals but I do use Calibre's news feeds and they do sort them independently. That date may be the key difference. I'm not at my computer at the moment to see if that is the case.
However, the Calibre people may have ideas on how to automate any changes you may need to make.