Your original question was how to work around this behavior without giving up symlinks. So I tried to help you find workarounds, and now you’re complaining about being given workarounds.
First, it doesn’t answer the question “Why does this happen in the first place?”
I would presume that it happens because, when the Find and Replace package was being developed, nobody ran into the bug.
Why does opening a file from Search Results result in a new file being found with the full, absolute path to the file?
I have no idea. I haven’t looked into it.
Sublime Text does not have this problem and if Atom cares about being competitive with Sublime Text (or any other text editor) then it is up to the software developers to deliver.
The great thing about open-source, freely available software is that it doesn’t have to compete with proprietary, closed-source, $70 software. It can, and for many people it does. There are some developers at Facebook who have built their own IDE on top of Atom because they could (there are also Juno and PlatformIO). Sublime Text I’m sure is great for people who want to pay money for professional support and a product that’s as perfect as it can be. Atom being as free and as flexible as it is makes it a valuable product in spite of its flaws.
I’m honestly surprised that there isn’t more traction on an issue like this.
There is an open issue. Another great thing about open-source software is that the community can share information about problems and if people like us are motivated to fix those problems, we can (and I have) help out in the area that is important to us. The dev team is very responsive and is hard at work on the things at the top of their priority list, but as it’s a free product, it can’t have a giant dev team. Atom is an oversized passion project that does not generate revenue and the people who work on it also have to work on things that bring in money. This issue is important to you, but it’s an inconvenience and it only affects a very limited subset of users. If you want to convince people that it is important for them to care about, you trying to guilt the developers because they can’t immediately address every issue is not going to be persuasive.