Commercials can be skipped via the remote. Comskip will run on your NAS (or whenever the DVR is installed).
It’s hard to recommend settings without knowing how you expect to use the app. If you’re only watching at home and have plenty of space, recording to mpeg2 without transcoding is just fine. If you want to use less space, transcode to heavy. If you don’t care about commercial skipping, you can turn detection off too. All depends on what features you care about.
For remote streaming of live tv, you can use the transcoder internetXXX setting on the extend by picking it in the app.
For remote streaming of recorded tv, it depends on what setting was used to record and what quality you want to stream at (which depends on bandwidth available). Usually bandwidth is limited so you need to transcode the recording either way, to save on data costs or deal with slow Wi-Fi.