AppleScript: How to open a file in TextEdit, without bringing the other TextEdit windows to front?
I think the problem you're having is that you've misunderstood what is actually going on. Let me try to explain...

The first question to answer is why were the windows missing from your first screenshot not visible? Obviously, the My Fruit Log.txt file was not visible because it wasn't open yet (i.e. your script hadn't run yet). But what about the other windows? There's only three possibilities:


TextEdit wasn't actually running (therefore no windows exist). This would be obvious - so no more discussion needed.
TextEdit was running, but it was hidden (therefore all windows are hidden). This just means you hid TextEdit from view. Running your script simply makes it visible again (along with all its windows except for any that may be minimised). 
TextEdit was running but all windows were minimised. This just means TextEdit is running but no windows are visible because they've been miminimed. Running your script makes the app itself visible and in the foreground again, but all minimised windows remain minimised.


In your scenario, it's almost certain that Option 2 applies.  So, while it's not what you want to hear, your script is actually working the way it's supposed to in macOS. The only way I can think of at present to achieve what you want in a practical way is to ensure that your script minimises all other windows except for the one it's just opened. For example, you could achieve this with the following code:

set targetFilepath to "/Users/Me/Desktop/My Fruit Log.txt"
tell application "TextEdit"
    activate
    open targetFilepath
    tell (windows whose id is not (get id of front window) and visible is true)
        set miniaturized to true
    end tell
    set bounds of front window to {279, 111, 1180, 719}
end tell


As you can see, I've just added two lines of code. I think they're fairly self-explanatory - They just tell TextEdit to minimise any window that meets these two conditions (1. it's not the front window and 2. it is visible).

Hopefully this works for you - but if not maybe someone else comes up with a better solution.