An older (20 Apr 06) article from the Jamestown Foundation's Terrorism Monitor speaks to this issue, although it is, by its own admission, a mixture of analysis and conjecture:

Christian Converts and Islamic Terrorism in the Philippines
...The Rationale Behind the Presumed RSRM-JI Nexus

There are at least four factors that would seem to have salience in terms of explaining the emergent nexus noted above. First, many BI members (the movement from which the RSRM is drawn) are either based in or have intimate knowledge of Manila. This facet makes Christian converts uniquely suited for carrying out attacks that are able to impact directly on the seat of national political, economic and cultural power....

...Second, and very much related to the above, because RSRM cadres do not originate from ethnic Moro Muslim backgrounds, they are less likely to be identified as Islamist terrorists....

...Third, and directly related to the above two points, it would be extremely difficult for JI to act independently in the Philippines given the enormous ethnic and linguistic diversity that exists across the Republic....

...Finally, since the RSRM is made up of converts to Islam, the group arguably has more to prove in validating the credibility of its jihadist credentials...
Personally, although I do not have the benefit of Pinoyme's local knowledge, I do not agree with his statement that convert terrorists would be "fish out of water" when operating in the traditionally Catholic areas of Manila, etc. Remember the key word convert. They were raised in the same Catholic tradition, and although they are now converted radicals, they possess the in-depth knowledge necessary to blend in when operational. Of course, this really applies to hard core terrorists; someone who is simply is a convert with radical beliefs would not be concerned with blending in and would stand out just as Pinoyme suggested.

However, the Philippine authorities are well aware of this threat, and the US has made significant strides towards effective sharing of intel with them in this regard. But the local authorities are certainly challenged by the manning and equipping issues in the spectrum of threat they face, from ASG and RSRM to the NPA and all the other various criminal gangs, pedophile sex tourists and just general crime in between.