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Most Intel GPUs are great at transcoding. Reliable, widely supported and quite a bit of transcoding power for very little electrical power.
I think the main thing I would check is what formats are supported. If the other GPU can support newer formats like AV1 it may be worth it (if you want to store your videos in these more efficient formats or you have clients who can consume these formats and will appreciate the reduced bandwidth).
But overall I would say if you aren't having any problems no need to bother. The onboard graphics are simple and efficient.