This guide will explain how to easily build doors inside buildings with snap in and without flooring issues.
Step 1 - Remove floor & roof in front of where your door will be placed and then place the doorway.
Step 2 - The floor won't snap into the gap because of the doorway.
Step 3 - Open the console* and type tcl to toggle collision off.
*- Console can be opened with ç, ~, ´, ö, or \. It differs between keyboard layouts.
Step 4 - Grab the door with Enter and then press Tab to cancel.
Step 5 - The floor will now snap in to the gap.
Step 6 - If any settlers walk into the building area, execute them.
You won't be able to place anything if there's an npc blocking the way. They will just come back if you command them to leave. You can also open console, click on them and then type disable to delete them.
Step 7 - Your shack can now have multiple rooms inside with no flooring issues.
If you're getting issues snapping in the door to the doorway just turn collision on again, exit building mode, then go back to building mode and it will work.
Now you can have closed bathrooms, bedrooms, etc. inside the main building.
PS: This also works with everything else. When you grab an item while your collision is turned off, that item no longer collides with anything else until you turn collision back on again, which means you can build anything in it or around it without that item getting in the way. That toilet for instance, just put a regular chair inside it using this method.
Bonus Tip: whenever you do this, the textures flicker a bit a the base of the door where the pieces overlap. To fix this, just select the doorway and use the command 'modpos z -.1' to drop the doorway *just* enough to stop the flicker.
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Credits: Special thanks to Alexandre for this tip.