I ran 16/4 to my windows, not Cat6. but after choosing QMotion for shades, I do wish I would have used Cat6 as it would have been cleaner. With regard to how to run the wire to the window during pre-construction, you have to decide if you are going with inside or outside mounted shades. We went with inside, so I ran the wire through the framing coming out the top sill 2” from the window and 2” from the right side finished framing (so the finished drywall). So you know, when you use QMotion in zigbee control configuration, all you need is power to the shade and for this, QMotion uses 3 of the Cat6 wires for + and 3 for - low voltage power. For this you can use either Cat6, Cat5e or even 16/2. It just depends on how universal you want your pre-wiring to be. Again, if it was me, I would decide on the shades now and wire for them.
Another trick I did. For all TV and computer locations, I ran an electrical outlet back to a switch in my AV closet. I then later rewired that switch to my UPS. Now all tv’s and related equipment is on the UPS and nothing flashes when power flickers. And, I do not need UPS in all my rooms.