Wrong precedence order for customizations vs. themes

[mcandre]

• [x] I am on the latest Hyper.app version
• [x] I have searched the issues of this repo and believe that this is not a duplicate

• OS version and name: macOS Sequoia
• Hyper.app version: 3.4.1
• Link of a Gist with the contents of your hyper.json: Defaults
• The issue is reproducible in vanilla Hyper.app: Is Vanilla

Issue

When applying a theme, then many of the options for customizing colors are blatantly ignored. The configuration loading precedence order is incorrect.

Please apply any configured themes, and then apply any custom colors to override the theme.