I don't see anything wrong with that.
If you overlay subtitles onto the video when transcoding, they will be scaled properly.
If you don't and also don't transcode the subtitles track, then there's simply nothing we can do.
If you don't but transcode the subtitles track then we may be able to rescale them but then it is not necessarily wanted either since rescaling the subtitles will also degrade their quality.