Hey Brett,
For the base design, WEBENCH optimizes the BOM list for cost and efficiency which means using a pair FETs can support the highest current rating of the design.
In the alternate component feature, it becomes a bit more custom so there are still chance you can find pairing of the FETs.
You question of why M1 has higher current rating than M2 is detected by the duty cycle of the design and that resulted a higher current is seen by M1.
At the moment, WEBENCH does not support muti-phase designs. I have stated that I will get you in contact with Eric directly and maybe he can help you.