Clipboard history records what the user copies. A feature that retains user data belongs behind an opt-in rather than being on the moment the input method is installed, and that is the stance this project already takes elsewhere: MSIME-Linux's PRIVACY.md says voice transcription is disabled by default and runs only when asked for.
MSIME-Linux already defaults it off. This is the only one of the input defaults that diverged where the Windows value is the one that changes; the other four are moving the other way, in metasequoiaime/MSIME-Linux#56.
Existing installations are unaffected. msime_setup.iss generates config.toml with onlyifdoesntexist, so this only changes what a fresh install starts with, and anyone who has already turned it on keeps it on.
The three values Prepare-PackageFiles.ps1 asserts about this file — schema, theme_mode and diagnostic_log — are unchanged.