Perhaps you can work around the problem like this:
Create an action which changes white to red, so you end up with an image which is black and red with transparent background. You could for example use Channel Mixer.
Run the action on all the images.
Trace to 3 colors with Ignore White ticked.
Expand the traced image.
I don't believe you can accomplish this with Illustrator's trace feature.
To Illustrator, white is the same as transparent. It sees them the same.
When tracing, if you don't ignore white, then white objects are created for both white and transparent areas. If you do "ignore white" then no white objects are created - and since transparent is the ...