A single word for not-full

I think "unfilled" would work:

• My bottle is unfilled.
• No unfilled spaces have been found.

unfilled

not filled

• an unfilled bottle
• unfilled spaces
• a vacancy left unfilled
• an unfilled order

Merriam-Webster

In the examples given by the OP, there is, in fact, no extra word required:

We add the grains to a silo.

I put the box in a warehouse.

He parked the car in a car park.

The fact of 'adding' 'putting' and 'parking' includes the information that there was space there in which to 'add' 'put' or 'park'.

That is why we have no word for the concept. That is why the English language has developed without a word to express what the OP is trying to express.

Language develops from concepts.