OP, as long as you inform your tuner what setup you have, there is no problem whatsoever. If you get too aggressive, the intercooler will definitely not be up to the task, and similarly exhaust pressure could be an issue with regards to turbo control and EGTs. Coming from a stock turbo, it will totally kick a$$ regardless, and put a smile on your face even without overly aggressive tuning.
Heatsoak in an intercooler is a question of thermal efficiency in regards to total energy flow through it. Its more of a gross flow issue than simply charge pressure. The stock IC also presents more pressure loss, thereby increasing charge air temperature pre-cooler, worsening the situation.