Now there are only 2 settings to customize current theme:
"workbench.colorCustomizations": {}
"editor.tokenColorCustomizations": {}

The downside: if you have a habit to customize each one of your themes, then you have to manually maintain the list of all of your tweaks.

New Syntax:

"workbench.colorCustomizations": {
    "[One Dark Pro]": {}
}
"editor.tokenColorCustomizations": {
    "[One Dark Pro]": {}
}

Color priority:

2: Setting with theme name ("[One Dark Pro]": {})
       ↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓
1: Setting without theme name (workbench.colorCustomizations: {})
       ↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓
0: Active theme (One Dark Pro)

Use cases:

• Using different themes for night and day
• Using several favorite themes (in no particular order)
• Trying out new theme, tweaking it, but in the end returning to the previous one