If the centre-back can find the striker through a line and the striker can receive in a useful position, I would encourage the pass.
Playing through midfield does not mean the ball has to physically touch a midfielder every attack.
The important question is whether the pass breaks pressure and creates an advantage.
Your midfielders still have a role. Their movement may be the reason the direct pass becomes available because they have pulled opponents away.
I’d explain the difference like this: bypassing midfield is ignoring useful midfield options without reading the picture. Breaking a line is recognising that the best route is available beyond them.
In training, give points for breaking any line with purpose, whether that is through a midfielder, into a forward or by carrying.
At U13, players should start understanding the principle rather than following a route.