Wilmer James, the C in the OP (not the utility guy) is actually a weird case.
If you don't like his 48 PC and you're an NL team there is nowhere to put him (except in RF as mentioned but hes not a great bat in RF which kinda undermines the point). You can trade him but what is his value? Not much. Meanwhile, almost every year you can find a washed up C who can still hit in FA who is at least as good a hitter as James and most of the time noticeably better (esp because there are plenty of switch hitting Cs). And nobody ever wants those guys so they cost nothing (<$2 mil for sure, normally closer to $1 mil)
Should he be in the majors if everything was distributed for peak efficiency on the world/macro level? Yeah. Is it that surprising that he isn't? Not to me.