The TH350 and the PowerGlide are the same size. It was introduced in 1969 to replace the PowerGlide. It uses the same output yoke and drive shaft as the PowerGlide, and mounts in the same location as the PowerGlide. The TH400 is a physically larger transmission (longer, taller, and bigger around, but it still fits in your car's trans tunnel without hitting anything if it was a factory option), and because it is longer the transmission mounting point is pushed further back in the car (1965-'73 cars all had dual holes punched to mount either a TH350 or the bigger TH400). The TH400 has a larger output shaft yoke (more splines) and needs a shorter drive shaft.
All transmissions are designed to mount flush; that is no washers or anything else that affects the rear mounting height. It should bolt flat to the mount, and the mount should bolt flat to the cross-member. The cross-member must bolt flush with the frame. If you change anything at the back of the transmission then you have to break loose and reweld on all the mounting brackets on the rear axel to maintain the same pinion angle that was set by the factory. Failure to maintain the front angle results in vibration in the drive shaft and excessive U-joint wear.
If your car has issues with the TH350 hitting the trans tunnel that tells you your body is sagging and you have to address the issue of rotten body mounts (what separates your body from the frame).