The vast majority of people need their TV signals to be transcoded to get it to H.264/AAC for playback on an iOS device, and it's much cleaner and more straight forward for the application to feed all the video streams through the same processing logic, so by default everything is transcoded for this delivery.
As you mentioned though, video from an HD-PVR is H.264 so in theory it could be delivered as-is, but a very small portion of the community is in this position, so it wasn't worth complicating the design to accommodate this scenario. Also, things are never that straight forward - I've seen native H.264 streams that just don't play on iOS devices (due to H.264 profile and level), so often need transcoding anyway.
There is also situations like you're wanting to record in high quality HD, for watching directly on your HTPC - but for viewing on iPhone/iPad devices, maybe your wifi network cant stream at that bitrate, or you're trying to stream it remotely over the Internet, where you need its resolution/bitrate reduced for smooth playback on the client, which would mean you want to do the transcoding anyway...
That said, you can probably force your setup to pass through the H.264 stream without transcoding it. You'd probably need to edit config.xml, setting the <TranscodeHLS> to something like:
<TranscodeHLS>-y [SEEK] -i [SOURCE] -map_metadata -1 -threads 0 -map 0:0 -map 0:1 -map -0:s -vcodec copy -flags -global_header -sc_threshold 0 -codec:a:0 aac -strict experimental -ac 2 -ab 128000 -af \"adelay=1,aresample=async=1\" -hls_time 3 -start_number 0 -hls_list_size 0 -y [TARGET]</TranscodeHLS>