Actually it is not even different tones in most of the cases. The definition of tones is this: https://en.wikipedia.org/wiki/Tone_(linguistics)
The tone doesn't change by slightly rephrasing a sentence or replacing an "." with a "?". This means that the derived intentions/personality of your character don't really change either.
Take some samples from the game and see.
And yes, the rephrasing is bad but what is worse is something that is not apparent at the first glance. What is worse for me, is that even when the choices actually differ a little, the NPCs in most of the cases respond to it in the same way/lead to the same consequence.
Let's compare to previous fallout titles for starters. TES is a very different story. All these skill checks in FO3 and (Obsidian's) FNV in the dialog which aren't in the game anymore beg to differ. There WAS an actual difference in many of the cases. And even when there wasn't, the NPC most of the times seemed to react to what you said and sometimes you couldn't even speak to him anymore because of the choices you made.