Well, if you are asking the script to run denoising, it will take longer :) Opening the image in the CIE with Denoise data that was saved for later does no denoising at all, you just have the regular non-Denoised image until you explicitly run the calculations based on the saved data. That is definitely the time consuming part, and if the scripting you are using invokes denoising, that is why running the script takes significantly longer, as the denoising is the time intensive part.
If you are just saving from the CIE without running denoising, that means you aren't using it at all and could have submitted the job to the render farm going straight to PNG (at least as far as the denoising is concerned, depends on whether you are adjusting any other post process things like tone mapping etc differently than what was set in the VFB, though it doesn't sound like it).