If you say, '[i]t does not make sense to have X'. you are implying that X is unnecessary and should be removed, even if you do not specifically request it. When you follow that statement up with, '[w]hat's the point of using it?', you may be asking a genuine question and expecting an answer from someone, but most people will read that as if you had said, 'there is no point to it'.
If you simply want to say that you don't think X has been used correctly, or you don't understand why the writer has said X, you can try saying something along the lines of:
I don't understand/see:
why the writer has included X.
what the writer meant to convey when he says X.
the purpose of using X in this sentence.
You could then ask:
Can anyone explain why they think it is necessary?
Does it serve any purpose?
Does anyone feel the same way?
Between these two questions you may wish to include a reason for your comments, e.g.
It seems to me that it does not belong in that sentence.
Logically X does not fit with the sentences either side of it.
X is grammatically incorrect within that sentence.
As for tone of voice, you can try bolding or italics, or you can enter a note in brackets, e.g. (irony), (angry), (puzzled), etc.
Or, you can keep your original wording, but add a sentence after them to clarify your intent. E.g.
It doesn't make sense to have X. What's the point of it? I don't necessarily mean it should be removed; maybe it needs reworded, or possibly rewritten.