You will likely need to grind a small lip of the subframe away; inline with the manifold. This will help insure no knocking ! Grind before fitting, re-paint to protect. 10 min job......
The reason the flexi's go in the original manifold; has alot to do with excess movement from soft engine mounts. After fitting new aftermarket manifold......fitting uprated powerflex engine gearbox bushes will stop the movement drastically and help to protect the new manifold / flexi
****I did this and had ZERO knocking / problems EVER.
However:
It is also possible to crank the engine forward on its mounts very slightly; which will increase the gap between manifold and subframe and give you more clearance.