Subtitles can be tricky due to the nature of MPEG recordings.
See this post on adjusting Subtitles sync:
Identify the type of sync issue you’re facing, is it progressive or constant and you can then adjust the settings accordingly.
What you want to do can also be done. See the advanced commands sections on how to delay cutting advertisements to AFTER the conversion, set PreConversionCommercialRemover=false
You may also want to refer to the UniversalCommercialRemover setting as appropriate.
As for burning the subtitles into the video use the SubtitleBurn=true command in your profile