Not sure why no one sees this, so maybe I'm wrong, but the seam on standing seam is not sealed, just snapped together, so water will simply flow into/under the top of this boot no matter how well sealed it is. OP started it's already leaking, and of course it is, there is no way to seal this properly. I put the same boots on my roof and made sure they didn't span a seam, works great. OP your roofer doesn't understand the fundamentals of standing seam. You are correct you probably need to replace both whole panels and relocate the vent or get a metal roof specific vent flashing.
Not sure why no one sees this, so maybe I'm wrong, but the seam on standing seam is not sealed, just snapped together, so water will simply flow into/under the top of this boot no matter how well sealed it is. OP started it's already leaking, and of course it is, there is no way to seal this properly. I put the same boots on my roof and made sure they didn't span a seam, works great. OP your roofer doesn't understand the fundamentals of standing seam. You are correct you probably need to replace both whole panels and relocate the vent or get a metal roof specific vent flashing.