You got a bit ahead of me on the itinerary, and I still don't fully understand it.
I did not expect that you would book your hotels this early. It is definitely not necessary.
However, it is certainly a good way to put pins in the map.
I looked back at the post where you last listed your itinerary, on January 17th, at 12:23 AM.
<<"September 11 train to Basel
Sils Maria 4N (via GEX)
BE to Lugano
Luzern 3N (via Centovalli Express)
October 3 train to Paris from Luzern via Basel">>
Picking up on your comments about good hiking, I agree that you have done that well. The exceptions are Lugano, where you might not wish to take the time to find a hike, and Basel.
First- has the Lugano to Luzern leg been changed to the Gotthard Panorama route? You know my opinion. I think that is the best choice vs. the route via the Centovalli line. Whether you take the boat from Flüelen to Luzern along the route is a matter of personal preferences. I would do it, unless I were pressed for time.
The whole trip is nice, but the boat ride's best part is from Flüelen to somewhere past Brunnen, as far as maybe Vitznau.. Not that the remainder is not a good ride. It is. It is just that the last part may seem a little slow. But, you can look at hiking maps if you get tired of looking at the surroundings.
About 1 hour+/- by train from Flüelen to Luzern, vs. about 3 hours on the boat. How about partway? Not so good. The only logical place to take the boat partway, get off, and then pick up a train is awkward.. It is at Brunnen. The train station is a 10 minute walk from the ship landing ( bus usually meets the train). And you cut short some of the nicest part of the lake. I'd stick with the boat, myself.
2. Night in Basel.
I have to ask "Why?"
The 1055 train from Paris Est seems like the logical choice. If so, it takes about 4 hours to Basel and about 7 hours to go all the way to Wengen. You can arrive at 1749. Basel is not a hikers paradise. It has some great art museums and historic churches. It has the Tinguely Water Sculpture ( Fountain).
The old town is not much, in comparison to Luzern, for example, or Bern. If I were doing it, and had no specific known reasons to stop in Basel, I'd go directly to Wengen, adding a good part of the next day for experiencing the Bernese Oberland.
The train journey is similar in length ( time) to the one at the end from Luzern to Paris.
And, it could allow another night at the end, in Luzern, or along the way. If you want another city, run up to Bern when you are in Luzern or Kandersteg or Wengen ( on a cloudy day). In my experience, either one is a much nicer city to walk around in than Basel.
So, offering my opinion, unless you have specific reasons that make it the right choice for you, I recommend skipping Basel entirely.
For what it is worth....;-)