On a track day on a summer's day that might be an issue, but in 90% of road driving scenarios, heat soaking an S3 intercooler would take some doing.
Dyno cells don't have anywhere near the amount of cool, fresh air going through the IC as the open road, so I wouldn't always take a dyno operator's word on IATs being too high. They might well be, during 10 back to back power runs in a tiny little room!
And then of course there is the volume of the thing to fill, which can increase lag a bit. That's why the S3 intercooler is only marginally bigger than the GTI one. VAG focused more on improving the core than outright size.
I think ~ £260 for a brand new 6R/S3 intercooler from the dealer is a great upgrade & OEM quality, even on a K04 for stage 2. Even better if you can find them on ebay for a steal!
Whilst the Peron, Welly boots, APR, Integrated Engineering & Revo ICs of this world have their place.... sometimes they're not necessary for the job in hand