At 100 yds, which is still a long distance to be expecting much even from a .32 conical, I don't think you will need a 36X scope. A 3-9 power Variable will give you more than enough magnification to reduce or eliminate human errors so that you can maximize the group size reduction. Use what you have, of course.
I know several shooters who put scopes on MLers, and Lever action rifles to work up loads, before removing the scopes to use only the Iron sights that come with the gun for hunting, and general shooting. Like you, they want to have an idea how accurate a given barrel is with a chosen powder/bullet combination. There is Nothing Wrong with finding out.
To answer your question, I am sure that on some guns, a scope and mount will affect the harmonics some, but I doubt the effect will make an accurate barrel shoot poorly, or an inaccurate barrel shoot well. Most MLing barrels are Octagon( I don't include those unmentionable things that some people call a MLER), and an Octagon is much stiffer than any round barrel, until you get at least 2 calibers wider in diameter on both sides of the bore.
You surely have noticed that some of the best modern ROUND barrels have flutes cut into them to help Stabilize them. The barrels are wide for the small caliber rounds they shoot, and the flutes do to the round barrel what an Octagon barrel already does. The shooters talk about " dissipating heat" better with a fluted barrel and other " benefits", but the true benefit is that it stabilizes the barrel for those high velocity bullets that are forced through the barrel.
An Octagon barrel is a series of triangles, over lapped, to stabilize the barrel and allow fore- stocks to be hanged from the barrels without adversely affecting harmonics or accuracy. The larger Octagon barrel( per caliber) also dissipates heat quite well.
Please post your results when you have fired those groups using the scope. I am sure all the members will be interested in what you find out. :thumbsup: