Whether Bukowski cared about changes to his collected poetry during his lifetime is a question that only he could answer, but he stopped doing interviews a long time ago, so we will never know.
As has been well-documented, he was quite angry when he did notice the changes in the first edition of Women, which he made Martin revert in all future printings. So my assumption, and I have to believe the assumption of John Martin, is that he would have cared. Why else would Martin wait until Bukowski died to begin his methodical campaign of destruction?
And if Bukowski could see what Martin has done since his death, we can only imagine that he would not be pleased (to answer your question about Linda, she has been made aware of what happened, and she is also not pleased).
You say you see changes in War All The Time, and I'm sure they are there. There are changes in all of the books. But those changes are nowhere near the scale and stupidity of the changes made to the posthumous collections. But yes, they have always been there, and you can find them if you look for them.
I don't imagine Bukowski sat down with the book galleys that Martin sent to him and sharpened a bunch of pencils and spent days comparing the printed versions to his manuscripts. There's nothing in his letters or writing or interviews that suggests that he spent a lot of time dwelling on his past work. That doesn't mean he didn't revise and rework poems, he did. But he didn't (often) revise them years after he'd written them.
As for where the manuscripts came from, there are 1500 in the database now, and another 1,000 waiting to be added. So I'm afraid I couldn't tell you, in most cases, where a specific manuscript came from. They came from people, universities, museums, even John Martin, who sold more than a thousand manuscripts to a bookseller in the 1980s, almost all of which eventually ended up on eBay. So they come from all over. We've been gathering them for 20 years.