The reason for the file permissions remaining unchanged is that the HostFS filing system does support changing the actual file permissions under Windows. It
should be easy to fix this (it requires an amendment by the author).
However, the clock problem is a little more complicated. The reason is basically the same. The emulator must provide some kind of interface from the RISC OS side of things to the PC side. AFAIK, these things are memory mapped which means RISC OS at a low level, writes values to specially mapped areas of memory to change the clock. I haven't a clue where the clock would be mapped into memory, or that it is even constant between machine boots. The net result of this (if I'm right - I'm not even sure of that) is that it becomes very difficult to provide this function in an emulator. And for something as simple as this, I doubt it's worth the time putting it in. Besides, the clock functions under Windows aren't all that hard are they?