There is nothing magical about whether the hard disk drive is installed internally, or using an external enclosure.
In fact, most HDDs in use today in consumer equipment use the SATA interface, which has a specifically specified external cousin, namely eSATA.
USB Mass Storage provides similar services.
The operating system obviously needs to support the relevant attachment interface, but any modern operating system will support both eSATA- and USB-connected mass storage devices just fine. Windows 8.1 should absolutely not have a problem with either of these.
File permissions will be unaffected by the different attachment interface, for better and worse.
If you normally run Windows from the internal disk, and move that disk to an external enclosure and boot from a fresh installation on a new internal disk, and you do not have centrally managed login credentials (for example, through Active Directory), then the user account on the new Windows installation will have a different security identifier. Since permissions are tied to the security identifier, this could pose a problem, even if you name the account identically. If you are using NTFS encryption, it will not be possible to access those files.
The normal way of doing what you are after is to transfer the files from the old drive when it is being used as it always has been, to the new drive (which may be hooked up externally, depending on circumstances). However, there is no technical reason why you can't do it the other way around. Just make sure to first fully turn off NTFS encryption for anything you want to be able to transfer.