Before any of that, this needs fixed beyond just the misalignment. I didn't realize how broken the "combine" option was when dealing with a large number of images. I think the problem is that when the total image count exceeds 64, an alternative method is used which doesn't seem to be working (at least not with the images you provided). Once I get it fixed, I can see what I can do about the requests. The transparency one may be tricky, no matter what a "dummy" image will need to be used. Internally, the script just uses ImageMagick "montage" to combine the images, so it will need a fully transparent image to reference for that space. I could probably generate one on the fly, but the dimensions would have to be a "guess" based on the images provided. All image segments should have the same dimensions, so it should be a fairly safe guess.
I have no estimated time frame on when this can be completed. I struggle for free time these days, and the combine/split code is a complex disaster that I have to relearn how it all works every time I work on it. These options were always niche with very few users, Admentus and GhostlyDark are all I know of that made extensive use of them so I only really tested cases for what they were using them for. Many of the options were tailored towards N64 virtual console textures, since it was the most practical use of the option, so its not much of a surprise its broken in other unexpected ways.
I have no estimated time frame on when this can be completed. I struggle for free time these days, and the combine/split code is a complex disaster that I have to relearn how it all works every time I work on it. These options were always niche with very few users, Admentus and GhostlyDark are all I know of that made extensive use of them so I only really tested cases for what they were using them for. Many of the options were tailored towards N64 virtual console textures, since it was the most practical use of the option, so its not much of a surprise its broken in other unexpected ways.