1) Freeview gives PCM or DD+ audio. The DD+ audio is only available on HD channels, and is pretty limited to films, recent dramas, that sort of thing. If using a soundbar, set the LG TV's audio to passthrough. I get DD5.1 audio from my T3-R via my LG TV to my soundbar this way. Sadly, I'm plagued with lip sync issues, an annoying LG issue. If you're only using the TV's speakers set the T3-R to PCM, stereo, or whatever it's called.
2) If you leave the TV on the relevant HDMI input the it should behave as you expect. However, a better way is to enable CEC in the T3-R so that when it's powered-up the TV will switch to the correct HDMI port. Optionally, as I recall, you can also have the TV power down if the T3-R is put into standby. I prefer not to use CEC, but it does generally work well enough.
3) See (2). Use the Manhattan remote. You can get simpler LG remotes to replace the Magic Remote. I agree, they do take time to get used to. eBay is your friend here. I bought a genuine (or so it seems) LG AKB73715601 remote from eBay for about a tenner. There are others out there. Just look for one that has the same set of buttons.
4) Picture settings are a personal preference. The T3-R has no picture settings to speak of, only the relevant resolution, HDR and so forth. Tweak the picture settings on the LG TV to suit.