It is worth noting that you agree that nowhere in Scripture does it state that animals or rocks have souls and will be resurrected on the last day. You try to appeal to an argument of silence which is the weakest argument of all. It would be like me saying that Jesus had six toes since the Scriptures do not say he had five toes.
If there are not specific and clear verses stating that animals and plants have souls (by the way, this is what the article is about), then all that is left are mere opinions, speculations, and imaginations. I do not know of anyone at any time in the history of the Church that has ever interpreted the verses that you cite as denoting that animals and inanimate objects have souls or will be resurrected.
Only the pagans had such belief in animal spirits and afterlife, such as the cat mummies that you find in Egyptian museums. I can find nowhere in either the Hebrew writings or the new Testament (biblical and extra-biblical) that the church held such beliefs, in fact they ridiculed these pagan mythologies and the worship of cats and dogs.
I've never claimed that plants and inanimate objects have souls. I have stated that our physical senses do not perceive all there is to God's Creation, and that the wonder of that Creation is much more than our ability to ever comprehend in the flesh.
As far as interpretations, you might want to look at Martin Luther, John Calvin, John Wesley and Matthew Henry, for starters.