Not with lithium batteries for use when riding. E-bike lithium batteries have battery management circuits which accept the charge current and distribute it to the cells, so it's impossible to draw current from them by that route. You could connect the charger to a pair coupled that way, but there would be no point since it would double the charge time.
To connect them for use during riding, the outputs have to be joined, the two positives together and the two negatives together, though that's best only done with a pair of matching batteries in the same state of charge.