Wardrobe wizard, as far as I remember, will deal with the differences in scale, position and geometry, carry over the rigging, and can carry over morphs from the original item. It will not create the JCM's of the target figure in the converted clothing.

Antonia uses JCM's quite a lot, typically in a Z-type transition curve generated by a linear relationship with output values limited between 0.0 and 1.0. The thigh-bend JCM is zero for aft bending of the thigh, then linear up to output value 1.0 at 60 degrees forward, and then constant 1.0 for the rest of the movement.

If the clothing does not have the JCM's poke-trough will occur of course only if the JCM is an outward deformation. The thigh-bend JCM for example on close-fitting pants will cause poke-trough on the fore side of the hip and thigh only, because that is where the JCM has a deformation working outwards. On the aft side the JCM models the flattening of the gluteus, and there will be no poke-trough, but the bending will be as ugly as we know from existing models, or even more because Antonia's joint parameters were designed to work with the JCM. A tight pant will hang wide if the thigh is bent.

Guess the solution for converted clothing would be a set of JCM controlled magnets miming the JCM; something similar to the 'magnetize' poses that come with the CP's G2 figures and with Victoria4. For a real conversions of the clothing, fit for general use, there is no alternative but to develop the JCM's manually. This also provides the possibility to fix unrealistic stretch.