The N249 bypass achieves a few things... it tidies up and removes a lot of pipes that have the potential to split and leak, improve the DV's response on lifting the throttle and generally clean things up especially if you are looking to tart up the engine bay a bit...
That said... bypassing the N249 then removes the ECU's ability to dump boost if it thinks there is an issue somewhere... N249 intervention tends to happen more on mapped cars than std ones... if bypassed and the ECU tries to dump boost (it will also throttle cut to an extent too) but can't due to the N249 not being in control of the DV then you will see a 'N249 mechanical failure' fault code...
The ECU also uses the N249 to improve part throttle response IIRC... not sure to what extent as my car has not been std for some time but the effect varies depending on circumstance and level of tune...
If you don't have to by pass it then there is no real advantage to it but on higher power stuff (bigger turbos and hybrids) then generally its binned off
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