Flush trim bits have bearings, some straight bits do not. The cutters on a straight bit are straight up and down, while flush trim bits usually have a slight angle to them. This angle gives a better cut because the cutter is slicing the wood off instead of hacking it off.
For most work they could be interchangable, but the better cut is from the flush trim bit.
For most work they could be interchangable, but the better cut is from the flush trim bit.