I changed an engine about 6 weeks ago, and after reading the post went
and looked to see what signs of the engine change might be visible.
The engine mount bolts actually don't look like they've been touched.
The bolt head shape doesn't allow a socket to touch the paint on the
mount, so there's nothing to see there.  Likewise the bolts on the bell
housing and a few others on support brackets, bell housing inspection
plate etc - they don't look like they've ever been touched.
I didn't take any special care to ensure that hose clamps lined up with
creases in the hoses the same, but it just seemed neater to line them
up, so there's nothing to see there either.
I know that I knurled exhaust flange stud bolts a bit, but after the
engine has been run for a couple of weeks, the shine on the knurled bits
have flattened off and darkened down so it's hard to see anything there
either, and at ~100k, then the exhaust might have been worked on anyway.
It seemed neater to reuse wiring loom cable ties, most of them were easy
to open, the replacement engine came with loom intact but cut, so there
was a spare for any tie that I damaged.  So there's no sign there.
Perhaps someone in a hurry might just cut them and use standard cable ties.
The car I did was a fwd so I had to remove the axles, so I could see
that the axle nuts have been removed and replaced and the old split pins
reused, but again at 100k they might have been removed for work on CV
joints/boots anyway.
The single and IMO most definitive sign is that there are minor paint
scrapes on the bottom of the sump - not from rocks or damage that could
have likely been done when the motor was in the car.  These probably
happened before I got the replacement engine.  The wreckers tend to
lower the engines on an old tyre or similar to support them, but the
sump still bottoms out on the ground, and probably twist a little as
they are lowered or lifted.
Apart from that, the engine and trans housing is a lot cleaner than I'd
expect on a car of it's age/mileage - but there wasn't any real need to
clean it that well - just me being a bit fussy.
I think that it could be very hard to tell.