well ultimately yes you will have to retune the ve tables for having the vvt on then as you are dramaticly changing the air requirements and using tps based ve tables your ecu will be very rigid in what it can do.
in effect you are then tuning a completely different engine.
it can only follow tps (y axis) and revs (x axis) and will only be able to react in relation to those e.g if the throttle reads 15% open @ 2000 rpm then it can only use that number. it wont know how much air is coming in.
if with your car running with the vvt off at wot at 3000rpm the ve table will say have a figure of 130ve lets say,
with vvt on at wot @3000 revs it will still read that 130ve value but with a larger air request from the engine creating your leaning effect because the 130% volumetric efficency will add the same amount of fuel as before to a larger volume of incoming air
i find it odd that webcon only use tps it is not regarded as the best way to govern a fuel map as there are soooo many variables that can be factored for using map pressures.
map like i say registers the actual inlet manifold pressure so can tell a bit more about load etc.( and indeed is the only safe way to map a turbo)
also it (on my setup) allows it to govern things like overrun fuel cutoff safely etc
my ve tables are map pressure based so there is a contingency of higher values should conditions arrise you do not expect.
the upper four kpa (y axis) lines of my map are never or rarely used and are in fact educated guess work knowing roughly what the contour is doing.
indeed i dont mind these areas running a little on the rich side as they dont get used and in that event wont cause harm.
my tb's are also cable based, now certainely in megasquirt terms the "closed loop" settings refer only to the pwm fast idle valve,
which is a flap valve that you bypass the throttle plate with (manifold side) which with the throttle plate fully shut allows enough air thro' to allow the engine to run and much like injectors uses pwm to hold it open at varying degrees for initial "vroom" when you turn the key then to a different cycle which sees it step to almost shut for cold starts.
without this the car was very hesitant in the winter, as far as i know the closed loop settings refer to this fidle valve being opened and shut to help with engine recovery/steady idles and has no bearing on fueling.
i know that when i say this that this family of engines seem to suffer a bit once you have pulled the etb off as this used to simulate what my fast idle valve now does with the throttle plate.
so i dont wether the closed loop will help this is definately a tuning issue because you are running tps map,