Well, some modifications are of general nature (dashes, cover). The change for the left margin is a conversion setting only significant for the mobi oputput anyway. So I think these three are fine.
I agree, however, the subscript changes are only significant for the mobipocket output, but I also do not know how to do this only for the mobipocket conversion. I am not familiar enough with Python and the recipe code to be able to do this. If someone has a suggestion, please go ahead. However, for now, this solves a lot of the problems I had with the recipe and thus I wanted to post it.
About your preference, I understand that you want the unmodified ePub but not all e-book readers understand this format, so the conversion approach also has its merit.