Depends on the spec you want to go for; there is no safe/not safe limit for engines. However with an AGU you are internally at a benefit from an AUM due to the large port head allowing better flow and the larger gudgeon pins on the little ends. For a K03 fitment turbo you will not need to do any internal modifications; for me a K03s can offer more than enough for an A3.
In my opinion (which is not shared by everybody, but who cares because I'm right) a good stage 2 A3 is as good as it gets. A safe and reliable 240bhp in a fairly decent FWD chassis.
The basic list of modifications would go:
S3 312mm brake upgrade (piece of ****, new carriers and new discs. Job done)
Forge 007p DV.
Jetex filter (off Bill at Badger 5).
Powerflex dogbone lower engine mount.
Stage 1 map = 190bhp and a fairly decent power curve.
K03s turbo.
3" downpipe and decat.
Silicone turbo intake pipe.
Front mount intercooler.
Eibach rear anti roll bar kit.
N249 bypass and PCV delete.
Yellow DV spring.
G60 flywheel and VR6 clutch upgrade.
Half decent rear section of the exhaust/backbox.
Half decent set of coilovers, personally I suggest Weitec.
Stage 2 map and 230bhp. If you can be ***** to throw a Forge wastegate actuator on there you can expect a bit more power across the range.
There are a couple of other tricks you can go, such as a VR6 MAF, WMI and large injectors to get the power up a little. But that's not exactly mainstream tuning and most people go for a hybrid turbo before they get to this stage. It IS possible to get 250bhp out of a K03s; but for the same cost you could get 270bhp out of a hybrid.
There is much more than the engine to stage tuning, IMO a stage 2 car is as much about the suspension and chassis upgrades as it is the go faster bit. So just remember everything has to be balanced and work together.
That should be all you need to be honest. Just make sure the car is properly serviced and up to scratch mechanically.