Principles of D.I.Y. Minecraft microworlds
There are two key ways these can "fit together":


Most obviously by size and connectors - all the worlds are built on 4 6x6 plates, and have a 1x2 with cross-hole brick at the bottom in the centre of at least two sides.
By theme (or in Minecraft terminology "biome") and features (forest, mountains, etc).


In terms of the four sets released, only two meet both of those:


The Village
The Forest (Ideas)


These both use the same shades of grey for the underground sections, and similar colours for the overground sections (greens, browns, etc.).

The other two sets represent completely different areas ("dimensions") within Minecraft accessed via special portals - there's no way to walk from a Forest biome to The End or Nether, so from a connecting point of view, neither of these really "connect" to the others.

So to create your own cells you'd want to follow the following guidelines:


Choose a Dimension (Overworld, Nether, End)
Work with 6x6 plates (or variants/multiples of)
Use a scale of 1x1x2/3 for most blocks (i.e. 2 stacked 1x1 plates) which can be capped with a 1x1 tile, for deep sections bricks can be used
Underground is typically 4 bricks tall, overground can be taller 
Transition between biomes nicely (Forest - Beach, Forest - Jungle, etc.)