Sorry, I just skimmed the messages, I may have missed things but I'm not sure this has been fully explained.
There are two orders:
- The mod order (aka deployment order) you set on the mods screen decides file overrides, meaning that if two mods contain the same file (or to be precise: a file at the same path) you have to pick which gets actually placed in the game directory. That is the equivalent of overwriting (or not) existing files if you were to manually extract the mod archive into the game directory.
If a mod has no file conflicts, setting a mod order has no effect (for any game) apart from making deployment slower. If you have a file conflict, Vortex will tell you. If you don't have file conflicts, you should not set order rules on mods.
- The load order affects which order the game itself loads the mods. Whether you can affect the load order and what effect the load order has varies wildly between games. Vortex offers automatic ordering with LOOT for the bethesda games because for those games it's practically impossible to predict or see the effect of wrong load order across the entire game so that a bad load order may reveal itself only hours into the game when you've already screwed up all your savegames. This is why the community treats it like some sort of black magic when really it's actually fairly simple mechanically.
For most other games, _if_ the game allows setting the load order, Vortex has manual drag&drop based load ordering with a bit of game-specific explanation.
For Valheim specifically (I haven't developed the game support so this may be bad information) I'm not aware of any cases where the load order between mods actually matters - either mods are compatible no matter how they are ordered or they aren't compatible at all.
For Load Order to be useful you need cases where two mods work loaded in one order but not the other and what many people don't seem to realize: This is only the case in a tiny fraction of mod combinations. Across all games, the common case is that the order doesn't matter at all.