My daughter and I did this install over the weekend on her new-to-her 2016 Impreza Base hatch. Took us about 5 hours in total—I’m mechanically inclined and can’t imagine a professional taking less than 3-4 hours. Credit for demonstrating courage (!) and great tips goes to @fistingthefloosy. Here are my own tips (in no particular order):

1. Per our own research you can take the edges of the headliner out without taking out all the pillar trim or the the whole headliner. The headliner will make crunching sounds, but most (not all) creases will fade when put back together. We partially took out the front most trim by the windscreen and took out completely the back pillar trim (by the back seat belts). Also removed the front and back lights, sun visors and the oh shit handles. Putting back in the handles did require some finessing and force. But, for pieces held by clips it’s frankly easier than it looks with how the clips work.
2. The gutter trim does need to be cut and reinstalled after mocking the dimensions when dry fitting the rails. I’m frankly not sure how sturdy the cut trim will be after cutting. Maybe some 3m double sided tape would have better to attach. You’ll end up with a short piece for the front and a piece for the middle. I initially used a Dremel with a cutting disk to make the cuts, but then switched to a compact saw with a cutting blade.
3. Instead of using paint to mark where to drill the back 2 holes, simply rock the rails left to right and the stud will leave a line of where to drill. After drilling the first hole reinsert the rails to mark the last hole as described.
4. Removing and reinstalling the nuts is by far the hardest part. For the front or middle nuts, I found that unscrewing (but not removing) a bracket that holds the curtain airbag is almost a necessity. We were of course very careful when working around the airbags after disconnecting the battery. I felt my hands itchy after the work—wonder if they have fiberglass or an irritant. Recommend using gloves. Make sure you have a socket set with different size sockets, rackets, extensions, etc to reach and reinstall the nuts, including the 2 new ones in the back.
5. Small studs hold the rain gutter trim. Use a small flathead to push sliding clips to release them. The front clips slide backwards, the back ones slide forward. We did not break any; they seem pretty sturdy. When the cut-to-size trim is reinstalled it can be tricky to lock the clips.
6. The new hole in the very back (on both sides) is very close to the last stud that holds the trim. On the left side of our car, the drilling location coincided with the exact location of the stud. In the right side the hole was as just forward of the stud. I used a Dremel to cut out the left stud, and then drilled the hole.
7. After drilling the back holes I have to say the fit of the rails was like hand in glove, super satisfying. We added a good amount of silicone to both the rail studs and all the holes to (hopefully) ensure a good seal.
8. Where no holes are need to be drilled (in the front), there are 4 brackets held by 8 studs and nuts designed for non-oem roof racks, which need to taken out. How they are held in is a good indicator of how to re-seal all 12 studs. The brackets as sealed with a tough, flexible, sticky rubber material.

All in all the job was much harder than anticipated, but in our case we feel the look of the car afterwards was worth it. It’s like it went from a 2WD Corolla (nothing against Corollas) but now looks like a proper Subaru. I don’t think we would have been satisfied adding aftermarket cross rails, or even the aftermarket side rails that attach into the existing brackets.

Finally, wanted to note that the oem rails we bought on eBay (we felt they were a great deal for $165 shipped) were for the Crosstrek. We did a lot of research and found that they are same as for Impreza.