Minecraft – Guardian farm low spawn rates

In past updates, biome changes have been retroactive. I logged into my original singleplayer world recently to find it was now a snow biome.

You can use a map editor (such as MCEdit) or a game mod (such as Bukkit WorldEdit plugin) to delete the chunks you haven't built anything in. When you explore them again, they'll regenerate using the most up-to-date method.

If you really want all the latest terrain everywhere, use MCEdit to copy your base and export it as a schematic. Write down the world seed. Start a new world in Minecraft using the same seed, then exit Minecraft and use MCEdit to import your old base into the new world.

To start things with, let me clarify something from the comments on the question. Placed(fixed), in the world, blocks, items and even flowing water or lava, are not considered entities.

Per the minecraft wiki

Entities encompass all dynamic, moving objects throughout the minecraft world.

Here is a list of entities in minecraft: Types of Entities

The reason your wheat farm is not working, is because crops require at least one player to be in their chunk update radius.

Basically, your farm system works, but because the crops never grow, the villagers can't replant anything.

Your iron golem farm is working because, it does not require any player to be in its chunk update radius.

Events processed in spawn chunks

Some extra information on crop growth requirements: Crop growth requirements

Something to note about spawn chunks:

Spawn chunks will not be unloaded from memory, regardless of how far away a player moves, so long as there is at least one player in the overworld. All overworld chunks (including the spawn chunks) are unloaded 60 seconds after the last player in the overworld enters the Nether or the End.

In your case, I believe that the chunks do not get unloaded, due to your sending an item through the nether portal(items on the ground are considered entities).