Thanks for the additional details! It makes sense that filters can’t be applied even with the API – if you try to download a Look via CSV in the Looker UI, there is also no option to update filters:
The filters need to be applied to the query and run beforehand, like you mentioned with the run_inline_query() method you are using.
I’m not aware of any workarounds, other than applying the filter before the Look is downloaded with vis settings applied. I can definitely see why it would be useful to change the filter while you download! If you are able, it would be super helpful to our product team if you filed a product idea or feature request for this capability. Here are directions on how to do so in the Looker platform: https://www.googlecloudcommunity.com/gc/The-Kitchen-Table/Feature-Requests-How-your-feedback-makes-Looker-better/m-p/592042