The site won't remove transparency from an uploaded page, will it? Will it be displayed over a white background?

Honestly, I have no clue. We could certainly try it though if you have sample images.

I just asked omn0scient (the webadmin/sysadmin for the website) on IRC, he basically said it goes like this:

Thumbnails remove transparencies, but full size images (whether chapter pages, "Images" posts, or forum embeds) should render just as they are. So if the full size has transparency, so would the rendered full version.

I don't recall which one it is off the top of my head but there should be a Homura x Madoka doujin on the site already that has some bonus pages at the end with one being partly transparent.