As far as I can tell, the choice of 32bpp RGBA vs. 24bpp RGB png export cannot be made directly in Aseprite.
To see the png export source code:
The following are guesses based on a quick glance at the code above:
Do any of the sprites that save to 24bpp have a Background layer in the timeline? (A background layer’s name is underlined in the timeline.) If the sprites do, and you want 32bpp RGBA, then try converting each background layer to a regular layer and re-export.
If that doesn’t work, when you save as a png, try going to File > Export > Export As. Set Export for Twitter to true. This will also set the alpha of one of the pixels – likely the one in the bottom-right corner – to 254.