My best guess is that you are correct. The throttle linkage pivots off the left side of the block. I expect that either the rod the goes forward from the accelerator pedal or the vertical rod from the bell crank to the carburetor are rubbing against the headers or whatever exhaust pipes had to be fabricated to fir the header.
I have never been a fan of putting Fenton’s on these cars. You have encountered the main reason. They “fit” but not really. My friend has them on a ‘54 3100. In order to fit the exhaust system the shop removed the bottom cover on the clutch housing. The second is that I never could understand why I should spend all that money just to make more noise and gain maybe 2 horsepower. Unless you are doing head work, installing a performance cam, and changing the intake system, you do not gain much.