Though it could be technically possible, it's probably not financially responsible. It would likely cost more than an automatic 1999 Subaru Outback with a rebuilt engine. The main problem would be in changing it from manual to automatic. Or, there are no automatic/manual "engine's", the engine IS separate from the transmission, this is an easy swap provided you have th skills, the wiring harness and ECU will need to be swapped as well.
The 2002 Subaru Outback has a flat 4 engine.
The 2014 Subaru Outback has a flat 4 engine.
The 2006 Subaru Outback has a flat 4 engine.
The 2004 Subaru Outback has a flat 4 engine.
The 2003 Subaru Outback has a flat 4 engine.
The 2005 Subaru Outback has a flat 4 engine.
The 2007 Subaru Outback has a flat 4 engine.
The 2009 Subaru Outback has a flat 4 engine.
The 2013 Subaru Outback has a flat 4 engine.
The 2011 Subaru Outback has a flat 4 engine.
The 2001 Subaru Outback has a flat 4 engine.
The 2008 Subaru Outback has a flat 4 engine.