Mod settings always show pending changes with disabled mods

[AMPW]

Game Version​

2026.10.25.5707

Operating System​

Windows 11

What Happened​

When disabled mods are present the game settings always shows the mod tab as pending changes which forces a game restart for any changes made.

What Was Expected​

Mod settings shows pending changes only if there was something changed.

Reproduction Steps​

1. Start the game with a disabled mod
2. Open the settings

Reproduction Rate​

Always

Additional Info​

AI description:
During startup, ModLibrary.PrepareAll() skips disabled mods before assigning their saved State and Index. Disabled entries therefore keep Index = -1. But ModManifest.IsChanged() checks every entry and considers it changed whenever Index != its position in the list.