It does mean you need to transcode and store twice as many files, which can be a serious pain if you've got a number of different bitrate H.264 assets. It can be a big pain if your software assumes there'll only be a single media file. Not insurmountable but painful for small operations (and for large operations, where there may be a back-catalogue to worry about)

I'm with you in spirit, but in practice I think we can all understand why people often just go for H.264