From what I can see, all these "iTunes alternatives" (iFunbox, iExplorer, DiskAid, TouchCopy...) offer pretty much the same access to "App file sharing" folders and to whatever's allowed of the file system. Is keeping timestamps of files/folders that are copied using these tools possible in any way, or is this also one of the limitations? It would make it easier to compare if the files transferred to the iDevice had the same timestamps as their originals on the computer; but they are timestamped with the time of transfer instead.
(I know I can keep timestamps in sync with WinSCP over SSH, for instance, but that's only possible on jailbroken devices.)