A single word for not-full

I would conciser one of the following for your particular case:

• Capacious
• Ample

In review, capacious seems particularly applicable in this specific context as based on the definition from www.dictionary.com:

Capacious: Capable of holding much; spacious or roomy.
For example: "A capacious storage bin."

But I think the key here is to realize that the magnitude qualifier is dependent on the specific context.

You would probably not use a word like "empty" or "full" to describe the air contents of a balloon. In such case you would probably more likely use "deflated" or "inflated". The fact that "empty" or "full" are generally quite broadly applicable does not necessarily imply that there exists a word in between that is also broadly applicable. Though perhaps it should, if indeed it does not yet exist. Definitely an interesting situation.

Cheers,
Arty

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Edit: Swapped in two new word suggestions that might fit more appropriately for the given context than the ones originally suggested ("growing" and "developing").

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.