The Oxford Dictionary Online has a number of different definitions of the word filter ranging from the original concept of removing contaminents or valuable particles from liquids to the more metaphorical "move slowly" applied to traffic or a group of people as in "The players filtered onto the pitch."
The use of 'filter' on the StackOverflow thread is a technical one specific to data processing. Obviously if you 'filter' a dataset for one value, then 'filter' the resulting set for the same value you will return all the elements in the resulting set, even if the resulting set contains one or zero elements.
This is different from using a physical filter (such as scientific filter paper) on a contaminated liquid where repeated filtering can remove more impurities than filtering once even though the grade of filter is identical. This is because physical filtering is an analogue process and some marginally sized particles can be missed at the first pass.
You express concern that 'filter' might be applied to an empty box or a box containing only one object but that is confusing only because you are applying the IT term to the real world. In IT you can apply a filter to a set containing only one element, an empty set or a set containing none of the required elements and you return either an empty result set or a result set with only one element. However in the physical world no one would talk about 'filtering' the contents of an empty box or a box containing only one object, the term would have no meaning in that context.
In answer to your final question the answer is 'no' in general terms, people do not talk about 'filtering' one object. They might talk about filtering mud, for example, to retrieve a single gold ring they knew was lost in the mud but they would be talking about removing the gold ring from the hundreds of thousands of particles and billions of molecules of water making up the mud, a very different thing from retrieving a ring from a box containing only that ring.
'Filter' has, as I said, a number of different meanings and the IT term is one, very specific one which does not apply outside the IT context.