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I have no idea really what is better, sorry. My only experience in this area comes from the times of PRS-500 which I sent them twice - problem with the screen, both times device was under warranty and both times it had custom firmware. They fixed the device without a single complain leaving firmware intact.
Since you cannot make a backup (assuming everything else is OK) and backup procedure does not root device and does not leave traces (all I do is mapping complete flash as a storage device rather than mapping various partitions as original Sony's firmware does) - I do not see how you could get in troubles.
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