There is nothing problematical if you stick to the definition, and don't philosophize so much.
The definition of work involves a force applied over a distance. To apply that definition you have to specify which force (exerted by what on what) is meant.
But that's a misconception about friction, not about work.
The definition of work involves a force. If that force is exerted by A on B, then the work calculated using that force is the work done by A on B.
All those statements are fine and I wouldn't disagree with them but they only work in a world where no one has a problem with their intuition. Of course we can do the Maths and come out with an answer. Many of us have no conscious problems with applying strict logic to every situation we encounter. But the fact is that an awful lot of people who post about this topic do have problems with it. Is there really any point in telling them that they just shouldn't? Isn't one of the aims of PF to clear up this sort of thing, rather than just re-stating what is 'obvious' to the cognoscenti?Right, so you can compute 3. directly from 1. and 2. without the need to pick a sign.
The OP has asked a question in terms of someone who doesn't 'just get' the problem and would probably appreciate more than just a reiteration of the text book line.