The split second is only used to control timing and activate the xtra fuel pumps. It does not affect injector pulse or map timing. For this reason the adaptive of the OE computer will not be affected. I saw the post you are referring to in your post. I may be correct as it goes to the VEC2 although I am not 100% convinced of it.
Paxton adds fuel by adjusting the fuel pressure as the engine starts heading towards boost only. When the car is driven normally and boost is not attained timing and fuel mixture is controlled 100% by the stock computer, therefore not affecting the adaptives fuel controls. As boost is being attained it ups the fuel pressure therefore adding more fuel, at the same time it removes timing to protect the engine. When at full throttle, the stock computer goes open loop mode which uses a preprogrammed injector pulse or fuel map and timing map. Because the adaptives are not changed by the split second, at less than full throtte, the adaptives do not change and therefore the open loop map is not affected.
On my own car I used both the split second and the VEC2 with out any problems. I used bigger injectors and the paxton fuel pumps. The split second was only used to control the fuel pumps as the car went into boost and retard the timing. Because the injectors where bigger I used the VEC to reduce the pulse by an just a percentage to make the adaptive stay equal too factory.The VEC II also allowed me to add timing when I saw a dip in the graph at 3400 rpm . I did not experience the problem that mention by you in this post
Oem adaptive problems (I believe this is the problem you are referring too). I have experience what he mentioned but it was fixed by adding more grounds for the VEC II.