I know what you mean. Using SE for creating/editing srt's, I don't mind much how it looks in my preview because the end goal is to play it with mediaplayers.
And as for srt, which is only text and timing-info, I always end up creating SUP files to mux with video. That way I control how & where the subtitles will look.
Maybe there is some settings withtin the DirectShow configuration you can change for how subtitles are displayed?
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