Re Harmony Companion - I believe you get a remote with the Harmony Companion? So you would just add this to your MyHarmony account as a new remote and copy your devices and activities across. But I must admit I have only skimmed this option - in prep for the day either my remote or Shield dies!
Re Flirc - Given you can get these for $40 I reckon its worth a crack - albeit it might need some set up, but there seem to be a fair few posts out there to check for guidance.
Re Sideloading - Yep no worries as long as there is a compatible Android TV version of the app. I use File Commander to sideload.
Re Manipulating Skins - Dunno! :)
Re Vero - Have read very good this about this device in the past.
PS: The thread that PANiCnz posted above has been gold for me in the past: https://forum.kodi.tv/showthread.php?tid=252916