Thanks for the replies.
I don't doubt that I'm missing something obvious, but I'm not sure I explained it properly either. I fully understand that semi-flatten is for the semi transparency problem of a gif file. When I discovered it, I read the manual page of what it does. I was thinking of a different application for the general idea of "Replace partial transparency with current background color".
I'm always looking for quicker ways to render and probably was over simplified in my thinking here. When I hovered over the semi-flatten filter and saw the tooltip "Replace partial transparency with current background color", it made me think I could restore the semi transparent areas in the render with the color that was removed with "color to alpha", without restoring the background as it is now fully transparent.
Unfortunately I didn't give enough thought to the edges. If they contained any of the color I removed, they would be restored with full opacity as well and would give a jagged look. I realized this after trying to manually create the steps by using the "Threshold Alpha" filter.
So I think I jumped the gun a bit and apologize for not thinking it through completely before posting.