The wiki for Power BI Embedded states that filters can be applied when loading a report or after the report is loaded:
"you can apply filters when loading a report".
In the following use case, applying filters when loading the report results in duplicate filters:
define a report with some filters (report, page or visual level)
save the filters as a JSON
when loading the report, apply those filters from the saved JSON, in the configuration.
after it is loaded, the report now displays duplicate filters
However, if we apply the filters using setFilters, after the report is loaded, the filters are correctly applied and they are merged by the API (the report displays only one filter with the value set using setFilters).
We would expect that the filters set when loading a report are also merged by the API.