You are right
with *.png-Format it works - as long as the transparency-index is >= 0
The transparency-Index is the Color-Number in the "Palette" left side of mtpaint.
As long as the image is in Palette-Format (indexed), you can find the color-index-number for transparency there.
If you choose/change your image to RGB (16 or 24 or 32bit per Pixel), it can happen,
that the colour you want to give transparency isn't in the palette. In that case
open the PaletteEditor(Ctrl+W), in the left column klick the colour-number, where your
transparent-Colour should be stored, then klick the pipette and in the image a Pixel of the transparent-whish-colour.
With "ok" you close the palette-editor and now you see your whished colour in the palette left side
and you can use that palette-colour-number when "save as" in the transparency-index-field.
If you have your image in RGB-Format (=16|24|32bit), you can also set the Alpha-Value
in active-Forground-colour (topleft) to zero, and paint with that colour into your image,
so that those pixel are transparent, or for example set the value to 128 the pixel is half-transparent.
BUT not all PixShowingPrograms do a rgbA-check. In my mtpaint-3.5 I had first switch
in menĂ¼ Channels to EditAlpha, check the box 'set' and klick 'ok'.
Example:
--> open mtpaint new.
--> Menu-Image-'Convert to RGB'
--> Menu-Channels-'Edit Alpha' check 'set' klick 'ok'
--> click topleft in the red carret (aktual Foregroundcolour), change the Alpha-Value from 255 to 64
--> Choose the tool 'Mask selection' drag a carret in the image, a little smaller than the black picture
..............................................................so that there stays at all 4 sides a rest of the black
--> click the 'Fill Selection' - Tool
................................... all pixels in the carret gets the transparency(Alpha) value 64 (to the actual colour there = black)
--> click topleft in the red carret (aktual Foregroundcolour), change the Alpha-Value from 64 to 144
--> Choose the tool 'Mask selection' drag a carret in the image, a little smaller than the transparent-Area
...................................so that there stays at all 4 sides a rest of the black and of the transparent pixels
...................................click the 'Fill Selection' - Tool, all pixels in the carret gets transparency(Alpha)-value 144
--> Menu-File-'save As' select File-Format:'PNG' save the image at a place you can find it
...................................(the transparency-Index can have any value, -1 also works)
you can test the image now for example with Inkscape.
->open Inkscape, paint a big blue carret
->Include the PNG-image (Menu-File-Include)
->move the image over the blue carret,
you can see, that the black colour of the image lets shine through the blue from behind in two different brightness
Now go back to mtpaint.
--> Menu-Channels-'Edit Image' (now - after have used EditAlpha - you can paint with Colours AND different Alpha-Values)
--> click topleft in the red carret (aktual Foregroundcolour), change it to a lightning green and change the alpha-value to 200
--> choose the tool 'Mask selection' drag a carret in the image, over all colours, but keep also areas of the black-Colours with Transparency
--> click the 'Fill Selection' - Tool, all pixels in the carret gets color lightgreen and alpha value 200
--> menu-File-save
to test it, go back to inkscape, delete the first test-image, include the new one, drag it over/around the blue carret.
you see, the green is there, if it stays over the blue, it let shine the blue a little through.
But again, the transparency with the colour-Index-Number in 'save-Image' works nearly everywhere, but only 100% transparent or not transparent and only for one single colour.
With the Alpha-value you can give more than only one colour transparency, and in addition fine-tuned transparency from 0(100%) to 255(no transparency), but not all software respect alphavalues.
Hope it helps a little