I think in the RO case, the value you see before you colonize the planet is the maximum production rate of RO. After you colonize, you see your current RO production rate, which is zero if you haven't learned the first rank of Advanced Mineral Collection. I believe the percentage quoted in the skill listing, at least for AMC, are percentages of the planet's maximum production rate (which you can't see anymore). The first rank of AMC both "activates" the ability, and increases your collection rate from 0 to 3% of the planet's max.