@AKUMA01 Hello Akuma and welcome to the new forums .
I took a screen shot : http://prnt.sc/d7xmbt as an example for you and every manager that might read this topic.
You are right my friend, the red squared players in a certain line up equal to players used in a different possition than their official one.
As you can see on my screen shot I used 2 attackers, one is placed on his normal attacking position and the other on the midfield.
A manager has of course the ability to use any of his players at any position that he wishes, but gets to see the red box as a reminder or warning that this decision may affect this player's performance during his match. The ideal is to use each player at his rightfull position but of course in some extreme situations ( like you said , if we don't have enough players for the right line up ) we can take our chances and use a midfielder as a defender or an attacker as a front midfielder etc. It's better to do that instead of leaving a position in the line up completely empty . But mind you my friend: when you do that the power and effectiveness of your player is not calculated by the OSM engine in the same way as it would be while placed in his normal position.
Good luck mate and enjoy your game and the forums!