Well, from where I see it, the question is valid since there are occassions where two terms may be used indistinctively.
"If" may be replaced by "whether" in sentences such as:
I will go even if it rains or snows.
I will go whether it rains or snows.
But not in:
We can go tomorrow if you want.
So the question: "Does "if" mean the same as "whether" in these sentences?" would be a correct and probably necessary question for a learner.
Also, some words may be perceived as "the same" by most native speakers, even though they could imply different things that most people is unaware of. For example: "north" and "northern".
That city is north France = outside France.
That city is in northern France = in the north part of France, not outside of it.
Though, I do not know any native speaker that would make a mistake using those words, I know very few that would be able to explain the difference (I might just not know enough language oriented English speakers).
On top of that, there are expressions that are used under certain circumstances due to protocol, but would be unlikely to be used in a different scenario, though they mean the same thing. A secretary may say to a person on the phone "the line is occupied", but if she is calling from home to her brother and his brother is talking she will not say "the line is occupied", she will say "the line is busy", so the learners will also wonder under what circumstances each should be used.
Finally, certain words or preposition could change from one variant of a language and another. In certain area of England people say "I have to take a decision", whereas most of the English population would say "I have to make a decision". So a learner, after seeing this kind of expression, could be wondering if both mean the same, if they mean a different thing, if they are both appropiate, et cetera.