You may be right; the devil could really be in the details. I am not a linguist, so I won't pretend to be more knowledgeable than you, as you may be one. I am generalizing about the location of the islands, relative to the other islands of the pacific. If in fact Polynesian is not even close to chamorro, then maybe the tectonic plates got shifted a little off. I have a friend in Cal who is a linguist, who happens to be guamese of filipino descent. I remember him telling me that he took up linguistics because he was fascinated with the similarities between the two native languages, and the shared words that came from spanish.
Actually, the Chamorros (and their native language) are about as closely related to Filipinos as they are to Polynesians.
More precisely, from a linguistic standpoint, the Philippine languages are quite archaic derivatives from the Malayo-Polynesian stock; they do not seem to have shared a common history with any other Austronesian language since the time of Proto-Malayo-Polynesian. Chamorro is linguistically somewhat more closely related to Polynesian, as both the Oceanic group (which includes Polynesian, Micronesian proper, and the Austronesian Melanesian languages) and Chamorro belong in a subgroup of Malayo-Polynesian that also includes the Austronesian languages of Indonesia, Malaysia, Madagascar, and Palau. In other words, there appears to be a deep linguistic divide between the Philippine languages on the one hand, and the "macro-Indonesian-Malaysian" languages (which include the outlying Austronesian languages of Madagascar and Oceania) on the other.
However, in terms of genetics, all populations who speak languages belonging to the Oceanic subgroup of Malayo-Polynesian (
i.e. Polynesians, Micronesians, and, especially, Austronesian-speaking Melanesians) have significant amounts of (racially) Melanesian (aka Papuan, Australo-Papuan, Australoid, etc.) admixture. Most populations of Indonesia from Flores and Sumba eastward also exhibit about the same amount of Melanesian racial affinity as Polynesians (of course, the Papuans from Irian Jaya are mostly Melanesian from a genetic perspective).
The Chamorros, however, seem to be more purely Indonesian (Austronesian, non-Papuan, non-Melanesian) than the Polynesians, etc. in terms of genetic ancestry.