1. The rules are the same for all apps.
2. Not Apple’s fault that Electron does not use the perfectly good browser engine shipping with macOS, but instead includes a separate browser with each app.
3. No one is forcing you to use the Mac App Store.
The private APIs rule is not new, Apple is just enforcing it harsher. Chromium has been breaking it at leisure, because Chrom(e|ium) itself does not ship via the MAS.
Yes, the people shipping Electron apps via the MAS have put themselves in a tough spot by skirting the rules. I can sympathise, but pretending that this is just Apple being mean and they couldn’t have seen this coming is downright disingenuous.
As for Safari, it would certainly be nice if they adopted new browser standards quicker, but being slow on the uptake is not the same as actively making things difficult.