1) A Clone copying a permanent from that expansion?
2) A creature equipped with Spy Kit?
3) A card from the specified expansion that is copying a permanent not from that expansion?
Rule 700.6a and such mention "the same name", but the Oracle text of the actual cards doesn't.
Quote from "Rule 700.6a" »
One card (City in a Bottle) refers to permanents and cards with the same name as a card originally printed in the Arabian Nights expansion. Those cards are...
The rule is not saying that those cards have "same name" in their text. Those rules are defining what the Oracle text of those cards actually means.
To have a better context:
700.6. Some cards refer to cards originally printed in a particular set.
700.6a. One card (City in a Bottle) refers to permanents and cards with the same name as a card originally printed in the Arabian Nights (tm) expansion. Those cards are...
So what those rules are trying to say is that the text "cards originally printed in {Set Name}" in those three cards is to be understood as referring to cards with the same name as the cards listed. City in a Bottle refers to things with the same name as cards printed in Arabian Nights, because rule 700.6a says it does.
What matters here is only whether the nontoken permanent has one of the names given in C.R. 206.3a, 206.3b, or 206.3c, as the case may be. A permanent's name (or names) is determined after continuous effects are applied, including copy effects and text-changing effects (C.R. 613.1, 109.3). Spy Kit's name-changing effect is considered a text-changing effect (C.R. 612.6).
EDIT (Mar. 12): Minor correction.
EDIT (May 1): Deleted second paragraph, which merely clarified the matter due to the old Oracle text. In Amonkhet, the Oracle text was changed in the three cards in question to refer to "a name originally printed", rather than "cards originally printed". Added rule citations in first paragraph.
EDIT (Oct. 4, 2018): Some rules were renumbered with Dominaria and Guilds of Ravnica.
EDIT (Sep. 4, 2019): Clarification.
EDIT (Sep. 24, 2020): Some rules were renumbered with Zendikar Rising.
Would they affect:
1) A Clone copying a permanent from that expansion?
2) A creature equipped with Spy Kit?
3) A card from the specified expansion that is copying a permanent not from that expansion?
Rule 700.6a and such mention "the same name", but the Oracle text of the actual cards doesn't.
To have a better context:
So what those rules are trying to say is that the text "cards originally printed in {Set Name}" in those three cards is to be understood as referring to cards with the same name as the cards listed. City in a Bottle refers to things with the same name as cards printed in Arabian Nights, because rule 700.6a says it does.
So 1) and 2) are affected, but 3) isn't.
EDIT (Mar. 12): Minor correction.
EDIT (May 1): Deleted second paragraph, which merely clarified the matter due to the old Oracle text. In Amonkhet, the Oracle text was changed in the three cards in question to refer to "a name originally printed", rather than "cards originally printed". Added rule citations in first paragraph.
EDIT (Oct. 4, 2018): Some rules were renumbered with Dominaria and Guilds of Ravnica.
EDIT (Sep. 4, 2019): Clarification.
EDIT (Sep. 24, 2020): Some rules were renumbered with Zendikar Rising.