Don't worry about the tree roots. Unless the rocks are piled around the tree trunk very deeply, they do not hinder water penetration and tree roots extend out a significant distance from the tree base anyway. Likely the rocks cover only a very small portion of the root system.

Unless you wish to give them away again, I'd consider something like a dry stream bed if it fits into the garden design. While a dry stream bed may direct water/rain runoff during heavy weather, it is NOT a rain garden. Rain gardens are intended to slow runoff and allow it to be reabsorbed into the ground before hitting the storm drain system and that requires a special type of rain garden soil, not rocks.

Dry stream beds are great for filling in areas like outdoor faucets and garden hose paths. Or you could build a gabion planter, raised bed, or trellis:

@gardengal48 (PNW Z8/9)

This is what I'm working with. Do you think these rocks are okay there or too much area is covered? You can see the concrete pad in the bottom right of the picture, too.

Also, thanks for the distinction between rain garden and dry stream bed. Dry stream bed is what I should be thinking about here.

The rocks around the trees would not bother me at all.....except for effort involved in keeping that area clean, tidy and free of any weeds, leaves or debris. The roots of the trees I see in your photos extend out well beyond what the rocks are covering.