Let's put it shortly : you can't achieve what you want to do the way you're trying to do it. Let me explain :
you can't use network on your pi0
you can't make a partial backup
Pi3 and Pi0 are different architectures, therefore they are not compatible. You can't plug one SD to the other pi.
For whichever purpose, you'd need linux to copy anything on the pi0 sd card.
The only "easy" (ahem ... that is quite a relative meaning ...) would be to use a USB key + a USB hub on your Pi0 (because I guess your pad is a USB one ?). Recalbox can mount a USB key quite easily (check our youtube channel, the tutorial playlist).
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