So the question is, is it acceptable such a large value of
PAO.EnergyShift ?
It might be. The optimal basis does not have to be the shortest.
You need to check the total energies obtained with big and small
EnergyShift. The one with lower Etot is better by variational principle.
If 1eV shift gives you higher Etot, then better agreement is just an
accident.
You have to check the convergence vs. Energy cutoff, k-points.
I suggest you to use the existing optimized basis for Si (from SIESTA
site). Optimization varies the orbitals cutoffs to obtain the minimal
Etot. Moreover, the orbitals cutoffs in such optimizations are
independent, in contrast to the case of using PAO.EnergyShift, which
might result in much better results.