I really have been enjoying your posts. I agree there were two wyes (have observed on aerial photos when I have been working in that area). If you look at the 1908 and 1895 plat maps for the area the wye is entirely south of the section line that divides section 33 and 28. Now the same section line splits the wye. I also pulled out the Valuation map for Walton Junction and the interchange-connecting track is the line that is furthest right on the map. The valuation map also shows the siding up the middle of the wye that you have shown but on the valuation map it does not extend as far north. The valuation map also shows the northern wye layout. The valuation map is dated 1917. Based on the 1908 plat maps showing the wye to the south and the valuation map showing the wye to the north that means it was moved between 1908 and 1917 which matches you hypothesis that it was moved for the construction of the M&NE. Excellent detective work.
Cheers,
Mark