It may be a personal problem, but I have found enough bad spots in the stabilized wood to conclude that the plastic will not 100% fill the wood 100% of the time. Some wood is worse about this than others. Curly Koa is particularly bad about having fine lines, and sometimes bigger spots, of exposed wood showing through the plastic.
And, I have left enough stabilized wood as polished and without a finish to conclude that irregularities in the plastic won't show in some wood until after the pen has been used and there is a little surface wear.
Solution? I just go with the same process of filling the grain and finishing for everything, regardless of whether the wood is stabilized or not. The excess filler is sanded off where it isn't needed.