Is customization for the Moderate Houses planned? Like removing the Mineshaft / Chests / Items / Etc?

We add it if its needed. We weren't planning on it unless requested.

Are you using this as your initial house and don't want some items/blocks?

At the time I wasn't using the mineshaft, but I have started using it by turning it into a high tech bunker of sorts, where a lot of machines (and control systems) go. I also play in creative, so I don't really need the furnaces or chests, as I usually replace them with things like the furnace from Extra Utilities 2 and Refined Storage setups.

I am glad that you have found some use for it.

I can look at adding some checkboxes for the chests, mineshaft and chest item.

Might be a while until this get's implemented though. We are trying to get Repurpose up to snuff in terms of code and the curse page.

The following options were made available and have been released to curse forge.
Add Chests
Add Chest Contents
Add Mineshaft

They are defaulted to true.

Thank you!