If you own both Archangel's Staff and Manamune before reaching 750 bonus mana, Archangel's Staff takes priority and will transform into Seraph's Embrace. The transformation drains Mana Charge on other sources, but it can be recharged again.
The transformation passive is not unique, and you can have multiple Seraph's Embraces.
To work out whether this item or a Rabadon's Deathcap would grant you more AP, you need to look at your AP and mana stats prior to the purchase. Both give the same AP when 0.25AP + 150 = 0.03(Mana + 1,000) + 60. (This is assuming that the Rabadon's Deathcap would be your first, and that you would thus be getting the extra benefit from the unique passive.) In other words, for the Seraph's Embrace to give more AP, your mana prior to building it must be at least 8.3...AP + 2,000.
This means that, purely from an AP perspective, the first Rabadon's Deathcap is almost always preferable. Take the case of Janna, the champion with the highest base mana in the game. A decent build for maxmizing her AP without getting particularly ridiculous includes the Rod of Ages, the Mejai's Soulstealer and the Deathfire Grasp. These alone give her 540AP (with 10 stacks on the Rod of Ages and 20 stacks on the Mejai's Soulstealer), meaning she needs 4,500 mana for the Seraph's Embrace to give her more AP than the Rabadon's Deathcap. Her base mana at level 18 is 1,454; the Rod of Ages gives her another 650 mana, for a total of 2,104. This total is far short of the total she needs for the Seraph's Embrace to grant more AP.