And they allow an easy upgrade path for projects that were already bit-banging DVI on the rp2040. Other than those two advantages, I don't think there is any advantage to the SIO TMDS encoder over the HSTX TMDS encoder.
I get the impression that the SIO TMDS encoder was added to the design first, and there wasn't a good reason to remove them after the introduction of HSTX.
The nice part about using SIO seems to be that you can do the tdms encoding there. With hstx you need the output bitstream in the right format already which seems like you might be back to needing the CPU to do the encoding.
You can configure it to directly consume any line buffer with any pixel format, from 1 to 8 bits per color channel. It even supports formats with different numbers of bits per channel like 8-bit RGB322 and 16-bit RGB565.
i have the impression, that the main motivation for this project was learning the intricacies of TMDS encoding and providing an open implementation as reference for other ppl, who want to learn too.
there are too many black box electronics these days, so it's very much welcome to virtually open them up, by providing software equivalents of their operation.