Salt in dry ingredients versus salt in water?
Yes it does - here's the reason why:

Yeast need some salt to grow properly, but they only need a very small amount (see 3rd para of intro). When you added the salt to the wet mix (sponge), you made it into a high enough concentration to inhibit the growth of the yeast, so it didn't reach the log-phase growth that you would expect when generating a sponge mix. This delays how the yeast behave later in the process by altering the slope of the growth curve and allowing it to reach the stationary phase (where an essential nutrient is depleted) without ever growing at a fast enough rate to make the dough as you expect.

The reason there was no further improvement with longer incubation, is also due to the depletion of that same essential nutrient. Basically this is rate limiting, so the gas generated from growth is equal to the rate at which the gas is escaping from your dough.

When you mix the salt into the dry ingredients this volume change relative to the wet mix, dilutes out the salt to a concentration where the yeast can grow effectively, but they are still limited by what has happened during the sponge growth. Where the log-phase is delayed, it will take much longer to start growing rapidly, and there isn't enough free water in your dough to allow the yeasts to easily reach log-phase in the full dough, so this limits what happens with the final product.