to illustrate the problem better:

1- under gnome (other desktop environments should work too, if they
implement standard Farsi/Persian keyboard layout), from settings > Region &
Language > add "Persian" input source

2- switch to "Persian" input source

3- open firefox, go to  https://unicode-table.com and click on the search
bar, then press: Alt+d and then Enter to see the code point for the typed
character

4- set the gnome input source back to English

5- open Emacs, run M-x set-input-method RET farsi-isiri-9147 RET

6- press C-q Alt-d and compare the typed character (which is a latin
character with diacritics) with what you've got in firefox (which was a
Farsi/Arabic Character)

again, i used Alt-d as an example here, you can see a complete list in
attached images in the original email. (as another example try Alt-h)