"You can also Xyz Summon this card by using a Rank 4 "Utopia" monster you control as the Xyz Material. (Xyz Materials attached to that monster also become Xyz Materials on this card.)" and "Cannot be used as an Xyz Material for an Xyz Summon." are not treated as the effects of an Effect Monster.
Placing this card on top of a "Utopia" Xyz Monster is treated as properly Xyz Summoning this card.
The "Once per Chain, during damage calculation in either player's turn, if this card battles an opponent's monster while this card has a "Utopia" Xyz Monster as Xyz Material: You can detach 2 Xyz Materials from this card; this card's ATK becomes 5000 during that damage calculation only." effect is a Quick Effect. (It does not target. Detaching 2 Xyz Materials from this card is a cost to activate this effect.)
This effect can only be activated once per damage calculation. (It cannot be activated more than once in the same chain.) If "Number S39: Utopia the Lightning" battles multiple monsters during the same turn, you can activate this effect once during each damage calculation.