Genuine question, did you even watch Heynckes Bayern Munich side in 2012/13?
I only ask because anyone that did watch them knows the idea he turned them into a counter-attacking team at any point in the season is a myth.
He won the CL final with 60% possession. He won the 1/4 final against Juventus with 55% in each leg, they beat Arsenal with near 60% in the second leg. So there was only 1 round where they weren't dominating possession - the set of games against Barca.
Even in the famous Barcelona game though, if you look at the average position of the Bayern Munich players (they are the team on the left) you can see they had an incredibly high line, higher than the Barca line in fact and pretty similar to where we play our defensive line. That's not a counterattacking set up, which would be a very deep line, usually with 1 forward much higher up than the rest to work as an outlet.
Barcelona dominated possession because that's what Xavi, Iniesta and Busquets did back then, without fail. That doesn't mean that Bayern changed their entire style of football to become a team which sat back, absorbed pressure and counterattacked, which seems to be what you think happened.
Instead what Heynckes actually did was make the team really shallow so the defence and attack were closer together and flood the midfield, which incredibly ironically given how you think the 2 games exemplify the differences between the coaches, is
exactly what Pep tried at Anfield.
The result of having all those players so close is that Barca found it hard to play through midfield with all those bodies, and when they did lose the ball, Bayern had a lot of numbers to break.