You're assuming a lineage which did all its adapting to living in trees before it started to glide/fly. There is no reason why this should be the case.
Not so, I'm assuming it was adapted to living in trees. The article states that the feet were adapted to "running on the ground"; I asked you whether this was correct because I've not studied the fossils and don't really have the technical knowledge to determine either way anyhow. While we need not expect the features to be exactly those of perching birds, we should expect them to be those of a tree dweller not a ground runner (squirrels certainly do not have feet like those of dedicated ground dwellers such as deer, hogs or even capyburra). The "Trees Down" hypothesis does require that ancestoral "pre-birds" were tree dwellers, and this should leave us with feet adapted to tree dwelling.
The article may be overstating it's case; I don't know. But if it what it says is correct then I think this counts as a compelling reason for supporting ground-up. Although it is, of course, possible that the first birds were tree dwelling and Archaeopteryx then re-adapted for running on the ground.