The second issue is one of institutional capability. The two organizations are separate but unequal. BSA has a disproportionate amount of money, assets, and political capital whereas the GSA does not, and suffers for it. Conversely, the GSA is much better at dealing with the social reality of a changing America wrt LBGT and non-Christian scouts, whereas the BSA, despite recent movements, is still rampantly homophobic and Christian. Merging the organizations helps correct for the unique issues of each while creating greater opportunities for all scouts.
The fact that the two are unequal is actually an argument against a merger. It may also be well and good in theory, but in practice such mergers rarely go well. The Unitarian Universalist merger is a prime example. I am not a Unitarian dammit! I'm a Universalist who is a member of a UU church.