1) The current limit on the Pi3B should
eliminate the power glitch problem, assuming that the Pi's supply is rated properly (2.5A at 5 to 5.25V).
2) Injecting extra power for USB should
also prevent the Pi rebooting. If the injector disconnects the downstream USB from the Pi's 5V, supply glitches can't get back that way.
3) In either case it is difficult to guarantee what an arbitrary (rogue) USB device will do through the drivers when plugged in. To be 100% safe, prevent connection of external USB devices. If that is undesirable, accept the (probably small) risk of problems.
4) I don't think anyone can quantify the increased security of an extra supply over using the Pi's supply. Only you can evaluate the cost if something does go wrong, and therefore what level of risk is acceptable. But since the risk is probably not quantifiable, in the end you pays your money and takes your choice