To cut to the chase: we won't be storing recordings in any format other than MPEG-TS at this time. We have a philosophy of doing the absolute least amount of processing of the bits that we are recording as we possibly can to prioritize reliability above everything else. The more processing we do, the greater the chance that a bug is introduced that corrupts/ruins a recording.
To make this more concrete: recording MPEG-TS from an HDHomeRun is just a matter of reading data from the HDHomeRun and writing it to the disk without modifying anything.
We understand this is annoying that you would have to do another step, but we feel like it would be worse to have a recording fail at some point.