Maybe I missed it somewhere in the discussion, but: in the model of "calories in, calories out", is it assumed that all excess calories go towards building more weight?

It assumed that they will be either stay 'in' and build weight or they will go 'out'.

Taken as that it's true.

However there are quite a lot of ways that energy can go 'out'. I can sometimes produce enough heat while laying down and meditating to relax to sweat.

I'm weighing at the moment 55kg. My weight through the last 5 years was all the time between 53 kg and 58 kg.

There are instances where I lost a kg of body weight over night for no apparent reason. On the other hand throwing 800 kcal of maltodextrose per day into my tea didn't gave me an effect of my weight that I could see in daily tracking data even through I took it for months and then stopped with it.