when I try to use it I get all kinds of white around tiles that are not fully pixelated.
I lost you with those last few words.
In most cases you define a single, distinct color to serve as transparency mask. If it’s not 255,0,255 (RGB)/#ff00ff you need to check if it is black, or on rare occasions even white. When you import (or just load) a PNG image you should know what that color is, and check that Preserve Transparency option before saving.
Even if there’s another format involved, you can check for its properties when saving transparency, opacity and alpha channel. For example, IrfanView (free) pops out a heap of tweaks when you’re about to save a changed image, one of them is Transparent Color. I’m just pointing to you that it’s out there, and that you can use a different utility from your design app just for this matter.
