Swing axle transaxles DO have 2 drain plugs. VW did away with the second drain plug on later transaxles.
IRS transaxles only have one. The ring and pinion chamber and the transmission chambers are not separate (Early porsche, swingaxle or IRS) and all of the trans oil will drain from the one. When you drain, you may want to jack the car up to tip the trans toward the open drain.
The plug on the side is for filling. When refilling, the oil level should be just below that fill plug with the car and transaxle level.
Greg