After some more testing, here’s what I found out: Alpha Channel is lost when tiling is saved as .png, only 32 Bit .Png can have Alpha so that’s my user error. Save as .Tif instead.
However after tiling I realized the Alpha Channel is not applied properly, it is flipped vertically and from the wrong partition element. I. e. X0Y0 Alpha was applied to X1Y0. I learned that by comparing the original alpha mask with the created partial one and matched them up. I’m using WM Pro 3027 btw.
Edit: Fixed it! The option “import into landscape” was causing this issues for the maps, disabling it resolves tiling issues, the Alpha Maps however are put into the wrong tiles and are flipped vertically. So in order to arrange that it needs to be tweaked in Photoshop. Thanks for the assistance.