What are the best timings of adding flour and soda into batter?

Both effects you described are real, and the two goals of optimal leavening and optimal binding are mutually exclusive. So, it depends on what you (or the recipe author) considers the more important goal. If you find that your pancakes are underleavened, you should rest them less, or not at all. If the texture is not smooth enough, you should rest them more. But there is no way to get both advantages at once. So:

Is it worth leaving them

is a matter of personal preference.

The optimal timing for mixing is quite clear: mix all dry ingredients (including the soda) with the flour, mix all wet ingredients together until smooth, then combine. Adding soda after a rest doesn't help, it starts reacting immediately, you will just have trouble getting it properly dispersed, and will beat out its bubbles while trying to incorporate it.

Some help can be had from choosing other recipes. Baking powder is less susceptible to the "reacts too early" problem than baking soda. And some flours (and starches) hydrate more quickly than others. But this is not a matter of timing, it involves using a recipe which has been carefully engineered for the goals you have.

This applies to batters for pancakes in the broader sense (so not only American style pancakes, but any situation in which a liquid batter is poured onto a hot griddle or pan). It doesn't apply to cake batters, which are quite constructed, so no such generalizations can be made about them, nor can you change the timing the author prescribes. Pies (in the Anglo-Saxon tradition, but also other pastries that get translated with that word) are not made from batter, nor are they chemically leavened.