It is how previous implementations by other manufacturers which achieve the same end result work (Neumann digital mics, Zaxcom "NeverClip", etc.).. and, lacking clear technical information from Zoom to the contrary, the assumed way the F6 works as well. Without testing to try and determine how it is doing it and if it does introduce a problem or not, this kind of speculation is the best we have to go on at this point.
I have no doubt the Zoom rep you spoke with is well versed on user-level functionality of the recorder, but I doubt he really knows how it is doing this under the hood, nor well versed on the possible repercussions being discussed above. In any case, is not in a Zoom rep's interest to highlight these kind of potential problems in a yet to be released new product.
As for myself (acknowledging that the border between digital fuckery and digital blessings is a fine line, more gerrymandered than straight) I'm withholding judgement until we have more information.