I was reading something on the net about the layout of Stratford station
on the Central Line. I have been there before a few years ago, but I
don't remember the layout myself. The page indicated that it's possible
to transfer between Central Line trains and mainline trains across the
platform. Doesn't this imply that it's possible to board a tube train
without entering a fare-control area? If so, how does one get charged
the proper amount on one's farecard upon exit on the other end of one's
journey?

If arriving at Stratford on a mainline train and using an Oystercard to
continue your journey you need to touch in before boarding the tube (or
v.v.) - there are around 6-8(?) readers on each of the Central line
platforms.

I suppose the same holds if one enters the platform area from the station ticketing hall?

The whole station is a fare control area. The only entrance is owned and
managed by London Underground with a tube style gateline. There is a
second gateline between the Jubilee line and the rest of the station so
anyone starting their journey at Stratford or interchanging from the
Jubilee line will be forced to pass a barrier.

Validators on the island platforms are provided for transfer between
'one' services to/from the east and Central/DLR.

It's not the easiest thing to remember - IME, it's easy to forget to
touch in/out on the DLR if you only use it occasionally. Much better
when gates force you to touch in/out at system boundaries.

And how are you charged if you do forget to touch in?

Depends where you touch out. It could be anywhere between £1 and £5.
The journey will be charged in addition to any other journeys you made
that day which might have been 'capped' at a certain price. Worth your
while to rememeber.