Linux desktop apps should never have ALWAYS ON TOP enabled by default, that destroys desktop compatibility. No sane app does this.
Hiding the current line signifier and cursor when the mouse leaves the window, but the app *still has focus*, is completely wrong and destroys desktop compatibility.
Whatever reasoning you used for enabling these two "features" was misguided, and abusive toward the end user.
What possible gain do either of these have to the GUI? As asked, why do the Windows and Mac apps not also have this behaviour?
If the Windows version did this, you would have a ton of complaints, and rightfully so!