So how is Apple "leaving money on the table"?
Apple doesn't make and sell most of those accessories so they are giving any profits from them to others. Apple could charge a (bigger) premium for the bigger battery and increased durability. Apple could sell to market segments they currently are ignoring. It creates more means to market their product beyond "thinnest ever" (which is reaching it's limits) and denies a means of differentiation to their competitors. The business case and possible value added by doing it is a fairly straightforward case to make.
The market segment exists for smartphones with bigger batteries and/or more rugged construction. That's not really a debate. Whether that market segment is big enough for Apple to give a shit is a separate issue but there is ample evidence that it might very well be big enough.
It's very unlikely Apple would make enough profit by having an additional phone model for these people to justify the expenses involved (engineering, inventory, etc.). It's costly for companies to have more versions of a product, so it's only worth it if it brings them more customers.
You are correct about the cost considerations but that is EXACTLY why Apple over time has had to create additional versions of their products as they mature. That's why they ended up with numerous different iPod versions. It's why they have several different iPad versions. It's why they don't just have one model of Macintosh. If they fail to address these market segments then their competitors will sooner or later. People will not stick endlessly with Apple products if they can get better options elsewhere. We've already seen that when Apple almost died prior to the return of Steve Jobs. They may not have to do it today but sooner or later they probably will in some form or fashion.