Swiss pass at a museum use a day?

Yes. The Museum pass function of a Swiss flex pass can only be used on days you have validated the Pass for use, not on "intermediate" days.

https://help.myswitzerland.com/hc/en-us/articles/115001474629-Does-my-Swiss-Travel-Pass-Flex-entitle-me-to-half-fares-on-the-intermediate-days-

Thanks for finding that!