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The fact that it is possible to set them incorrectly is why, in some projects where I'm concerned about this, I'll add a small series resistance to an inbound signal. Should the pin become OUTPUT and driven in an opposing direction to the signal, the resistance serves to prevent a short through both devices. The possibility is always there, whether you ...
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There are some hardware-specific abstractions (they mostly define the maximum memory available), but otherwise these are functions are implemented by the C/C++ runtime (on arduinos an implementation called "NewLib") and usually "just work". You might want to take a look at this question, where quite a bit of background is given on the SAM ...
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