This is a known issue where the PDF output options will always be the ones defined at report level, with the ones specified when using Run Report With Options / Now being ignored.
This issue does not occur when scheduling the report or using Run Report With Options / Later.
Another workaround is to use views of the report. The report views properties can be changed in Analytics to use specific PDF output options.
If you only need one set of PDF output options and your report uses a different one, this can also be changed in the report properties in Analytics.