Unfortunately, even after 8 years, there's still issues with Total Integration. The timing issues are well known and documented on the official Access Virus Forum.
As for the stability of the TI OS: The more recent ones are all declared as "beta" although they are production quality. I had to install 5.1.6.05 because of switching to macOS (Sierra) and didn't run into any issues. Actually it seems a bit more stable than 22.214.171.124, but that could be well because of the better USB stability of Sierra vs. El Capitan.
IMO, the TI has tons of annoying issues, some minor, some major, but after all these years there's still no true competitor on the market.
Regarding your issues:
1.) have no clue
2.) should not be like that, TI2 is always recognized on my system, seems like a USB issue. Try a different port, or try a high quality USB 3 hub with MTT.
3.) yep, it's like that. Sucks like hell. Working with Cubase, it's always a lucky event when all the sequenced ticker synths from the Virus match 100% with the other syth tracks from Massive, FM8, Absynth and drum tracks from Maschine or Steven Slate Drums. Never had these issues with the VSTs alone.
4.) If USB is plugged in, the MIDI ports (and keyboard) are ignored. Can't remember for sure, but there might be a global setting where you can change that. You can do Local ON to make the keyboard work on the Polar/Darkstar.