The order of revelation is not part of the transcription, and what we know about that order is neither complete nor certain. This adds an uncertainty, in the case of perceived conflict, about what abrogated what. Since the burden of proof for abrogation of individual verses is pretty high by all accounts, this added uncertainty makes it more difficult to overcome that burden of proof.
Indeed. This became salient in the case of 2:234/2:240
. The claim acknowledged the dilemma that the abrogating verse precedes the abrogated verse in transcription. Some scholars claimed that the order of revelation was the opposite, but they had no proof. In fact, the majority of the scholars acknowledged that the order of revelation of these two verses matches their transcription order and thus they had to conclude that a verse may abrogate another that is yet to be revealed!! That's how desperate some of them were in defending a seriously flawed conclusion.