Some further tidbits that come to us via our counterparts in Japan.

Will there be repeatable quests that reward company seals?
We will continue to implement quests and content where you can obtain seals in stages from 1.19 on.

Once you join a Grand Company, will the seals you earned from the other two city-states be unusable?
Yes, you won't be able to use them. However, since there is a possibility that we devise future uses for those other seals, we will be maintaining your seal data behind-the-scenes.

As for the other discussions related to the choices of rewards offered between the Grand Companies, I will pass along your comments to the dev. team.