I often come across people who reject scientific facts and theories that don't fit into their own worldview. So when this worldview stems from an adherence to dogma, thus the reasons for rejecting science are because of a doctrinal presupposition, it seems only fair to say that science and religion are in conflict. After all, people are rejecting science for religious reasons.
As far as I can tell, the accommodationist sees it differently. Instead of the conflict being between science and religion, it's that the doctrinal presuppositions are a case of misinterpreting religion. After all, people who adhere to those same doctrines support science and its discoveries.
Partly my worry about the accommodationist position as I see it is that it's asking people to comment on the validity of another's approach to religion - that we're in effect needing to be mini-theologians and tell other people how to do their religion. And I'm really not sure to what extent we can do this. What's to say they're doing religion wrong? From the insider perspective, their view might be more consistent than the view I'm offering. And from the outsider perspective, the preference of a particular view is correlated to its compatibility with the outsider view.
Thus I find the accommodationist view hard to justify in supporting it. It's not to deny that there are those who have compatible religious beliefs, but that those compatible religious beliefs are compatible with those incompatible beliefs. A presuppositional commitment that necessitates an incompatibility won't go away because others don't take that presuppositional commitment.