I don't think it's odd at all. If you want Section 3 to apply to electors, you have to specifically identify them because electors are not officers. Senators and Representatives are likewise not officers (the Constitution only refers to "members"), and so they must be listed separately. But Article II repeatedly refers to the President as holding an "Office," so there is no need to single out the Presidency. No one thinks, for example, that the Impeachment Clause's reference to "any Office of honor, Trust or Profit under the United States" intentionally excludes the Presidency.
I agree with you on this. Separating the Presidency from all other offices/officers makes no sense. There is no textual basis for such an idea apart from hyper-literalism, which should have no place in interpreting the Constitution. As you mentioned, Article II includes multiple references to the "Office" in which the President of the United States holds. I don't see how the "Office of President of the United States" is distinct from any other office or officer.
I do think it's interesting as to how Section 3 of the Fourteenth Amendment is constructed. Disqualification is established as a matter of fact. (It does not define insurrection or rebellion. On the other hand, the last part is the definition of treason, which must be determined in a court of law.) However, removal of disqualification is very clear (a 2/3 vote of both Houses of Congress).