Magazines (kbin) and Communities (Lemmy) are the naming conventions for the group type of posts offered - like subreddits. Magazines and Communities are effectively the same thing, just different naming conventions from their different backbone software running on the instance.
Instances are the full server in which the communities and users are held. Like sh.itjust.works is an instance - it’s the page where you can log into in order to then interact with anything both housed within your instance as well as the greater fediverse (barring any defederated instances, as you mentioned).
Cisgender means the person has a gender identity that matches the sex they were assigned at birth.
If you are a man and you were assigned male at birth, you are cis.
If you are a man and you were assigned female at birth, you are trans.
Non-binary can mean anything from not having a strong specifically male or female identity to closer to switching identities (bi-gender falls closer into this) to just having a lot of serious fluidity, but typically speaking at least part of the time the identity doesn’t match the assigned sex at birth.