Trump is looking forward overseas partners and good deals to strengthen his domestic hand. That's probably why he chose to drop by the KSA in his first foreign visit. Doing business with them in billions should be easier than negotiating with China or other more pragmatic governments in East Asia.
This may give some leeway for Duterte to actually clean up the separatist mess at home once and for all. But, he needs to be quick and decisive.
Nonetheless, CIA is more than the US government, hence, what Trump thinks of Duterte may have no bearing on what the US power elites think of him.
In any case, a strong home base would make it more difficult for the US to intervene and threaten Duterte government.