Yep! Most microcontrollers will sustain permanent damage if you short an output pin for any significant time. You could probably design a microcontroller that didn't do this, but it would require putting a big resistor in line with the pin (decreasing responsiveness and max power output) and/or adding a lot of circuitry and increased cost to defend against a risk that's not a big deal when the chip is being programmed by a competent embedded engineering team.
Transistors that can handle a lot of current or voltage will need to be much larger than most of the logic transistors on a chip, so even though they may appear to be few in number on the schematic, they can add up to significant die area for a small part like a microcontroller.
This is a layer below the digital circuit abstraction in the territory of analog circuits and device physics.
The extra current is a physical thing and you need more material to temporarily withstand it, and more circuit to detect and control it. Since it's an uncontrolled switching event, it'll probably ring unless you add even more components to absorb and control that. Then that could exceed the physical limits and trigger a parasitic circuit that doesn't have an off switch, so you need yet another circuit to detect and shut it off somewhere else.
It can be a lot of work for the board designer to make it reliable and compatible, assuming the other chip it's talking to can also handle the extra current. It's cheaper and more reliable to type GPIO1DIR=OUT or whatever. Sort of like when you drive a car, it's easier to choose to drive in the correct lane than it is for the car to enforce it on you and protect you if you do it anyway.
> The extra current is a physical thing and you need more material to temporarily withstand it, and more circuit to detect and control it.
Supposedly most of the chips can already temporarily withstand extra current. But the point of a current-limiting circuit is that you don't have extra.
> uncontrolled switching event
I'm not suggesting turning it off entirely, unless that's much much easier.
> it'll probably ring unless you add even more components to absorb and control that
If it fluctuates some when overloaded, that still sounds better than frying itself. But I'd expect an integrated implementation to keep pretty tight bounds.
> that could exceed the physical limits and trigger a parasitic circuit
What physical limits? You've lost me at this point.