Hello,
So there is a way to do to say that in all variant with package1 the cost is 10 and if it is package2 the cost is 20 or i've to create the variant and changed it one by one??
The best solution will be to only use a characteristic for the "Package" feature, and use custom ITEM fields (business edition) and create 2 dropdown for your 2 other features.
If you only have the starter version, YES you'll have to automatically set the price for each variants, but your can actually use Mass actions to do it in "Mass".