Hi, I am sure that either way you go you will end up with a good frame. I myself will probably build this same project (the garden shed) this year.
One thought I wanted to add: in this project the floor joists are 4x6" which connect to pockets in the 8x8" long sills. The plans call for you to reduce the floor joist ends to 4x4". If you cut the floor joists now in green wood the ends will shrink somewhat in both width and height (cross grain) to something like 3.75" square.
Next year if you get your green 8x8" sills and you go to cut the joist pockets in them then I would keep the cross grain depth cut = 4" since the sill will shrink (you will have a little surface step until the joist and sill reach equal moisture content). However, I don't think you need to make the long grain pocket width = 4", I would make it equal to 3.75" or whatever width the floor joist end width has become.
It might be possible to do this elsewhere, in situations where you have long grain/short grain connections between members with different moisture content levels, just be sure that you keep in mind which way the wood will be moving as the moisture changes. Doing this should result in tighter joinery.
Anyone have experience with or comments regarding this approach?