2 in 1 with pen inside and thunderbolt, anything besides yoga x1

I don't think you'll find anything with a stylus that is kept inside the tablet. It's not so much because the tablets need to be thin, but rather because OEMs want the pens to be thick for ergonomic reasons.

As for Thunderbolt, there's the older Asus T303 that sells for cheap nowadays. Beware that the newer model T304 has no Thunderbolt.
The Miix 720 also has Thunderbolt.
These are a bit smaller than the yoga 920 since they're detachable 2-in-1s (Surface Pro competitors). The only one I know of this kind that has a quad-core 15W CPU and Thunderbolt 3 is the Thinkpad X1 Tablet.


On the same size as the 920 you have the Surface Book 2 13.5". It's more expensive than even the X1 Tablet, but any version with the Core i7 already brings a GTX 1050 dGPU within the keyboard.
Personally, this would be my ideal solution, and you can get one for as little as ~$1600 (i7 + 8GB RAM + 256GB NVMe + GTX 1050) in the US.

 

So, what happens when something in SB needs to be repaired? You need to replace the whole thing?

 

Might be too late for you, but I believe the Asus Switch 7 Black Edition clips the pen into the chassis on the side.

Some reviewers have commented that because of this the stylus feels a bit thin.

I almost got one due to the large size (13" screen) and I think it uses a Wacom digitizer. Unfortunately the battery life isn't great and the stand can be a bit fiddly. I ended up getting a 15" Surface Book instead.

Regards,
SB