No, A-Skills or Seals that boost stats can not manipulate the stat gains you get from merging.
The only thing that can affect the gains are IVs, as the gains goes, in order, from the highest stat at level 40 (base) first to the lowest stat at level 40 (base) last. Stuff like Weapon Might and, as you were asking, Skills don't get factored.
EDIT: Merge stat gains are based on level 1 stats, and not level 40 stats.
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