If you go to a suite's Application tab directly, not first clicking on Libraries, and switch it to a standalone app, you are not prompted to exclude non-platform-oriented modules.
(Long broken, just was not sure if it was already filed.)
Unfortunately difficult to fix, since SuiteCustomizerLibraries is written to use a Node hierarchy as a data model, rather than as a view over a separate model. Could perhaps make LibrariesChildren and all the stuff beneath it be held by SuiteProperties rather than SuiteCustomizerLibraries, in which case the logic behind DISABLED_PLATFORM_MODULES would be handled in SuiteProperties when BasicBrandingModel fired a change in brandingEnabled.
Too risky for 6.9 - would require substantial rewrite of this section of the customizer dialog.