You can just average ('stack', if you want to use a different method) images with Photoshop (convert layers into a single smart object and choose the right blend mode under the smart object options) or specialized astro tools like Sequator (free and easy to use).Does pixel shift make gigantic files? If so, I'd rather have multi-shot noise reduction that writes to .cr3 instead of .jpg. I've tried multi-exposure with 3 exposures averaged into one final image as a workaround, but that doesn't work--it causes DR to plummet.
Don't expect to much of a difference with just three shots, as noise is reduced by the square root of the images you put into. So for 1/2 the noise, you need 4 images. For 1/3, 9 and 1/4 16 and so on.