Haven't dropped a Subaru engine yet, but in my long experience with
Corvairs, which used a rear-mounted 6 cylinder boxer engine ranging
from 2.4 to 2.7 liter displacement.  Removal from below was the way to
go.  The transaxle was located forward of the engine, and the
drivetrain essentially a subframe in itself, and we found it very easy
to jack up (and support) the car and remove the entire assembly from
below by simply disconnecting the half-shafts, suspension links,
engine mounts, fuel and electrical connections.  An experienced pair
of backyard mechanics could do it in less than 2 hours, and I've known
people to accomplish it solo without spending much more time.  Of
course, cars of the 1960's had far less auxiliary equipment and much
better access to the hardware involved.  The Subaru drivetrain is far
more complex, but its low mounting may make this approach feasible.
Don't know how much more may be in the way and whether the subframe
that cradles the engine may be a barrier itself, but it's worth
investigating.

That's the kicker.  Doing it with the tranny attached makes for a much
less complicated reassembly.  However, pulling the engine and
transmission together from above requires clearance and angles you
probably won't have.  Of course, any removal with an automatic will be
easier than a stick, since disassembling and reassembling the shift
and clutch linkages can be as complicated as the powertrain and
require more precise alignment to function properly when you put it
back together.  Likely that separating the engine from transmission
and pulling from above is the way to go.  As you say, aligning the
input shaft is critical.  Interested in hearing how this project
evolves.