If your target is Kindle, PNGs aren't preserved when converted to a Kindle format. At least, not MOBI/KF7 or AZW/KF8. Don't know about KFX.
I unpacked the kindle formats made by Kindlegen and all PNGs had been converted to either GIF or JPG.
And no transparency, even in the GIF format which does support it.
So if I have a PNG, or an image that is basically linework, diagrams, text, or cartoonish art, I usually convert it to GIF myself so I can optimise it. Kindlegen passes GIFs through to the Kindle format unchanged (so far). I use Irfanview (Windows) for this, which can do stuff like resize, sharpen, change colour depth, edit the palette. And also convert transparency to white.
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