I never tried to fit a full size steel wheel in my trunk. That was one of the many things I was going to do to my Contour but never got around to it before I traded it off. I would suggest just taking one of your wheels off and sticking it in the trunk to find out. If it doesn't fit, here is a suggestion for you. This is one of the many ideas I have had.
I know that the trunk pan cannot be lowered, as there are emissions parts on the underside that are height sensitive. However, I thought about taking a thick sheet of particle board with some spacers on the edges to make it level with the edge of the rim if it wasnt thick enough and building the trunk up a bit so that the trunk mat would sit flat. All you would need to do is use the trunk mat as a pattern and cut the particle board in the same shape. Of course, you would need a hole cut in the center to fit around the spare tire. I know you said you weren't interested in modifying the trunk, but I thought that I would throw that out there in case the idea interests you.