Hi,
1. You won't loose your changes to that view file when you upgrade.
2. You name apple, but apple doesn't sell RAM and processor alone. They only sell the computer with the options, so you can do that with HikaShop options with characteristics and a none variant without the issue you mention of the none variant appearing on the product page of the option product on standalone since they don't sell it in standalone.
I'm not saying that options are not common, just that your needs are a bit specific compared to most shops.
3. Yes, if you don't have characteristics in a product that you use as an option, HikaShop automatically adds a "no" choice to the dropdown because of course there is no point in having an option dropdown where you only have one choice.