Well, I'm seeing this argument more and more in these discussions: Just don't use it...it's an option. Well, said option costs time and resources better spent almost anywhere else. Just keep in mind every time someone asks for a feature and Bioware accommodate the feature, something is being sacrificed as a result. Are you okay with this feature at the cost of a companion, romance, story content, side missions, abilities...?
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Yes and no.
Any change from the original approved game design is a deviation that uses unscheduled time and resources. However, said deviation can improve the game and thus gives value. Besides, the overall asset allocation includes extra buffers to handle the unforseen glitches, such as design flaws.
While something may be sacrificed, I wouldn't worry too much because giving up a stupid side quest is worth the change.
As you said, it really comes down to value, time and resources. If an idea passes muster, it gets implemented.