Normally in English, "where" type questions are referencing the relationship between 2 or more physical items and their relative location to each other. To answer a "where" question, one normally has to provide a second item to serve as a reference point for the location of the first item.
For example: Where is my TV?
Answers: On the table. In my house. In Texas. In the US. On planet earth. All of the above answers are correct to differing degrees of accuracy.
I think most people's definition of "where" in the above context is easily grasped.
However native English speakers, having fun with our language, will also use "where" to denote the status of non-physical relationships between non-physical "things".
In the case you mention, Britain while being a physical landmass, is also an non-physical idea, specifically a political organization of people (a nation) who happen to mostly live on the previously mentioned landmass.
The original question being posed is referencing this non-physical idea (the British nation) and is asking in relation to the EU (another non-physical idea, specifically a political alliance of nations) where will the British "stand". The "standing" is not a physical location, but rather an ideological "location".
Ultimately what is being asked by this question is, will Britain continue to have a constructive relationship with the EU after it ceases to be an active State in the political entity known as the EU.
Other examples that you might commonly see in the English speaking press that conflates physical location and ideological standing:
What nations will fall into the Russian orbit? Nations won't physically orbit Russia, but if they come under the political influence of the Russian government they will often be referred to as being in the Russian "orbit".
Will the UK and US become closer when the next president takes office? Again, physically their distance from each other will not change, but if the political goals of each nation become more aligned, then we use the word closer, which is normally related to physical distance, to denote a non-physical comparison in the status of our relationship.
Hope this helps and hope I didn't add to your confusion.