Based off of my own readings on zilvia and the Internet, I haven't seen people run into issues running the ISR downpipe, in fact, they say it hangs up well compared to the Megan flex DP and haven't seen anything about clearance issues.
Most likely the hybrid manifold is causing the issues. I'm sure you know this, but might be a good idea to secure the trans mount somehow, else those vibrations could be issues in the long term for your turbo studs and manifold.
This is all my speculation, correct me if I'm wrong about ISR downpipe clearance.
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