I agree with Radwraith. Low starting competence can be eliminated for those who don't like it by starting at a higher XP total, but if the game system has 'heroic' stats locked in on Day 1, there is no practical work-around for people who want to start small and build up.
Sure there is, it's just a little more work.
A Rogue Trader character starts with 25+2d10 for Characteristics. It would be no effort at all to say, "for this campaign we will be starting as junior crew members so everyone starts with only 20+2d10 in Characteristics." What might be harder is to have everyone start with fewer skills and talents, but really it would just be a simple matter of agreeing that a junior Rogue Trader doesn't have the Command Skill for instance.