Most aftermarket IC's will see a significantly smaller pressure drop. This could very well cause the boost control system to overshoot boost and result in wildly fluctuating boost levels which would feel like the surges you're describing. If you'd like to take some logs, I'd be happy to look at them for you and tell you what I think.
FYI, in general adding a bigger TMIC on a WRX with stock turbo won't result in any power gains even with a tune. I know this from experience
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Thanks
-- Ed