If an Arrow of Harming's base arrow damage is enough to kill while you're holding a Totem of Undying, the Harming damage is dealt after the totem activates. You can even bypass the totem entirely with only a Harming II Arrow.
Steps to Reproduce:
Run "/kill" to ensure you have full health and no player-assigned attributes.
Set the "naturalRegeneration" gamerule to "false" to avoid yourself from regenerating.
/gamerule naturalRegeneration falseObtain a totem of undying, a bow, and an arrow of harming with instant damage 2.
Hold the totem of undying in your offhand and the bow in your main hand.
Switch into survival mode and teleport yourself 23 blocks upward so that you have half a heart of health remaining.
/tp @s ~ ~23 ~Look upwards and shoot yourself using the bow and harming arrow.
Take note as to whether or not harming arrows can bypass the totem of undying.
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This is intended game design, You receive the arrow damage 1st, breaking your totem and the the instant damage effect kills you a second time
How it works != how it is intended. Totems are intended to keep the user alive after a hit. The player is hit once, not twice.
I can confirm for 1.16.4