That's odd; I never had any issues like these. Display ordering is always the same. I have two 27" 4K monitors: one connected directly to MBP's HDMI and the other through a USB-C hub (also HDMI). Connecting both always gives me the correct ordering, and it's instantaneous - it takes longer for the monitors to turn on than for macOS to distribute the windows, so when they're on, everything's in place.
macOS's display handling has been flawless to me.