Nothing wrong with that, first boot will be slightly longer, but safe either way. Letting the system decide which apps need to be re-optimized is just faster when it comes to first boot time after the update.
Normally done automatically by the system on first boot after an update, but could get interrupted in very rare cases.
Absolutely pointless, the system does that automatically.
Normally, either before flashing or after flashing the ROM, as long as it's before you reboot from TWRP to system (for immediate results), but unless you have some very specific issues (apps having abnormal names, or text being abnormal in certain places) it's not even needed.
Sure, it will be regenerated.