I tried with cat -A <file> and other editors to confirm multiple times that the issue is with geany editor only.
You confirmed what with `cat -A`, show all your workings, I can't see over your shoulder.
I cannot replicate any bug in Geany, if I open a file with a newline at the end the extra empty line is shown, if I open a file with no newline at the end no extra line is shown. This is what is the intended behaviour, and as far as I can see Geany is behaving as intended.
You need to provide an exact set of steps that demonstrate your issue, if it can't be replicated it can't be fixed.