That stat is deceiving because watching Shelton played, he was consistently get pushed back into the QB. With Limmer, he may graded lower because of the scheme and missed assignments. Time will tell with year two on Limmer. But strength-wise, Limmer can hold his own at the point of attack.
A large part of the stat is sacks, hits, and pressures allowed. Things like it looked like he got knocked over very badly or pushed back are a bit more subjective than questions such as "was the QB sacked?", "was he hit?", or "was he pressured to the point he had to move off his spot?".
Those questions are what PFF is measuring. As pertaining to Limmer v. Shelton, the rookie allowed sacks/hits/pressures at a higher rate than Shelton. That's why he was graded the lowest at pass pro in the league. PFF can't grade scheme and missed assignments because no one outside of the team knows precisely what the blocking assignments were.
As you say, the hope is that Limmer improves in his 2nd season. If he does he soundly beats out Shelton and we're all happy. If he doesn't, Shelton is an insurance policy.