Don't think of it as double-majoring. In most of those circumstances, you're progressing in those majors concurrently. Think of it as trying to remain effective as a computer programmer, though you haven't taken a course covering the new tech for a few semesters, while pursuing your biochemistry degree. The penalties only come into force if there's an imbalance in your classes, not if they progress together, with the PC (student) staying current in both classes (majors).
From a game design standpoint one of the major purposes it serves is to discourage the single-dip into a class for the initial benefits (improved unarmed strike and stunning fist, fast movement and rage, all martial weapons plus a combat feat, huge spell list for using wands, plus notable saving throw bonuses for all classes). And then favored class provides a free pass on that for certain cultural combinations. I like the way that works and think it was a worthy attempt.
The trouble was it was a penalty and if there's anything I've learned about gamers today, they don't abide penalties unless it's from their own dumped Charisma. So, as a mechanic, it was doomed to be house-ruled away.