Again, without knowing the conditions, that actually could be fair. If both cars were done back to back and idling during down time, perhaps the stock setup of three heat sinks sandwiched together really is creating Heat Soak Island in there and you're starting out with a thermally challenged system from the get go. Just removing the meat of the heat sandwich (even if it's still there, but not putting out it's own heat) could feasibly see a 30 degree lower starting point, and also allow the entire cooling network to retain better head room through out sustained pulls.
There are a number of high power cars with FMIC, so the constant assumption that any aftermarket stock location is preferable to any fmic seems to have been heavily challenged with real world results. If we were seeing consistent issues with a particular turbo and a particular intercooler, I think we could assume that there were limitations, but again, we're dealing with too many variables. I still hold that oil cooling is a major issue, at least for the GTI without the piddly external cooler the R gets. So if you're comparing an IS38 GTI to a stock R, you're already biasing the outcome just for that alone. I'd greatly prefer to tackle coolant, oil and charge air at the same time, trying to isolate one without addressing the others is sort of like adding a dogbone insert without adding motor or transmission mounts. Oops, currently there.