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Does anybody else feel like the mutations you can start with can make your character nigh-on invincible in the early game? And do you see any way to fix this?

Mutations are a reason for a crafty GM to seriously inconvinience the character. Remember... Know the Mutant, Kill the Mutant. Almost anyone in the campaign world should be going out of his way to make the mutant's life miserable

There is one form the 'Into the Storm' expansion that grants you +10 Str and +10 T..the name escapes me, as Hummel said, mutants are to be hated, hunted and purged.

A hefty chunk of mutations are horrible, horrible crippling things that gimp some characters forever due to an unfortunate roll on the table. And all of them, even the good ones carry hefty social stigma. If you're a mutant that isn't a navigator, you will have a tough time interacting with a lot of people and give inquisitors and such convenient excuses to declare your whole crew heretical if they feel like it. Besides, most every rogue trader character is overpowered, and they don't need mutations to do it. The PCs are supposed to be head-and-shoulders above most enemies, which is why the challenges tend to come from other sources besides "tough encounter with mooks" unless they are fighting daemons or super-Xenos.