I would not use Wonder Under in an item that will be microwaved. WU is basically a heat activated glue, therefor when the item is heated, the glue will melt again, and your appliques would come loose. I don't even put items that have Wonder Under in the dryer, for the same reason. The appliques come at least partially off, if not completely. Even if you stitched down the edges, it would still be attached unevenly in the center, causing an unattractive bubbling effect.
It would probably scorch also, causing discoloration at the very least, if not a potential fire hazard.