Your question rests on the premise that Germany wanted to "swoop in and take the philippines". The threat of German Imperialism, be it in the Caribbean or in the Philippines always loomed larger in the American imagination than it actually was. It also made a welcome excuse for the United States' own ambitions in the Philippines and elsewhere.

As far as I'm aware, there were no specific orders for admiral Otto von Diederichs ships in Manila Bay. When they realized that the Americans were there to stay, they eventually left. Germany certainly wanted to keep its options open in regard to the Philippines, but taking the whole archipelago was probably not what they had in mind. If there were German designs for the Philippines, they were probably similiar to the taking of Kiautschou (Tsingtao) in 1897: a base for trade and the German fleet, but no large-scale colonization.