How to match pystan optimizing effect?

PyMC3 has a much richer VI module than Stan, so it is hard to use the exact same algorithm. The slowness and inaccuracy is due to your parameter selection in pm.fit(...) (e.g., suboptimal learning rate, too many obj_n_mc, too few iteration) - you should try with the default first:

with model:
    mean_field = pm.fit(method='advi')