Finalizing Itinerary, need advice on Bavarian Alps

Hallstatt is beautiful, but so is Berchtesgaden, and the latter is much closer. I'm not sure you need to do both, especially as you already have a busy itinerary. Why don't you leave the Hallstatt day open? Give yourself some flexibility for weather and slowing down? This is the third week of your trip, and you all may need a slower pace.
The top of the Salzburg Fortress is a great viewing point, in all directions, tho my days for pix from up there always seem to be hazy. The walk across the mountain towards the art museum, and ending at the Augustine's Beer Garden, is another opportunity for pix.
My most spectacular , almost unworldly photos were the ones I took from the Konigsee boat ride, coming into and out of St. Bartholomew Island. The water was so clear, so reflective, there's the Alps, all shining back in the wake from the boat. I wish we had gone all the way to Salut.
Mirabell Palace Gardens are also a good setting for pix, along with the "SOM" Cemetery next to the waterwheel and bakery ( back in the old town.)
You have done a great job of research and integrating Forum input. The trip should incredible. Safe travels!

On October 3 you mention a salt mine. We’ve been to some in Austria before and I think there is an age (4) and height limit to go in the underground mines. If you select one of the two you mention check their ticket and admission policies to see about <3 year olds. I also like how you’ve kept some options open near the end of your trip for indoor or outdoor locations to help you be more flexible with your photography possibilities. Have a great, early fall trip.

@Pat, Thank you so much. Day is definitely open. We probably won't book trains until we're for the day trips, to make sure we stay flexible and maybe take it easier. Thanks so much about the advice for the photos. I'll take those definitely into consideration.

@mona, that is great to know about the mines. I will definitely take that into consideration.

Still plenty of photo opportunities at Neuschwanstein with the bridge closed.

I'm itching to get back to the Bavarian Alps, probably September of 23 or 24. It's easy to spend a week in any of the areas you mention. Although I take the odd bus or train, I always rent a car, so no expert on travel times by public transportation. If Salzburg is not written in stone, I suggest looking into Bad Reichenhall, a good spot for those using bus or train. It also has a large thermal baths.

Consider the zoo at Hellbrunn for your 3 year old. Also, one or two alpine coasters. These are in the area
https://www.hochlenzer.de/rodelbahn.html

https://duerrnberg.at/?option=com_content&view=article&id=57&Itemid=59

Choose the salt mine which fits into your day's activities, depending on where you stay.

Chiemsee is a very good day trip, allowing you to see the palace and its grounds, plus the abbey and a pleasant walk around the tiny island of Frauenchiemsee.

Werfen has the splendid castle and ice caves. Ramsau has the Wimbachklamm and the iconic church of St Sebastian.

A whole day can be spent at Königssee if hiking is your thing, but not for a 3 year old. You can combine Königssee with a cable car up the Jenner (photo opportunities).

I'd give Neuschwanstein a miss, unless you happen to be in the area at another time. The best shots to be had of Neuschwanstein are if you cross the bridge and hike twenty to thirty minutes up the hill. I found this out later – since the bridge is closed, you can take a cable car up to the top of Tegelberg and walk back down towards the castle to take the same shots. The problem with this is you have to walk back up with your 3 year old.

Thanks so much @Gundersen. So many more options! I will definitely take the zoo into consideration, although Washington Dc has an amazing zoo that we visit pretty often. I will definitely consider those stops.

Thanks everyone for the amazing feedback. i'm still torned between keeping my itinerary the way i planned. (even though a lot of people get disappointed by Neuschwanstein i kind of want to see that for myself instead of regretting on not going)

Or just dropping everything after the Konigsee lake on October 5th and replacing it with Werfen, Prien, Mittenwald as a day trip from Munich and maybe something else? I wouldn't see the palaces or GA-PA, but i wouldn't need a car that way and I would stay always in the same area as opposed to changing bases to GA-PA