My installer did not install a threshold with T&G interlocking.
In fact the flooring is all misfit and the veneer is all splintered and uneven.
The threshold and the flooring boards are not even and it’s the bathroom
Entry. So it’s bad.
How can this be properly repaired?

Also, what’s a good putty t use on all the mismatched gaps?
I need something that will last.

If there are splintered edges, those boards need to be replaced. Splinters are dangerous walking with bare feet. Hopefully this can be resolved.
Most wood patch or putty needs to be coated to keep the color.
There is a special" pre-finish" type of wood patch that dries hard and doesn't need a coat of finish to protect it. It is water-based and will shrink a little so large gaps need to be filled twice. It comes in many different colors and can be mixed together to make a certain color if you don't find a good match. Woodwise is one brand.
A reducer strip at the edge of the flooring could take the place of a threshold so the surface is smooth. Sometimes the reducer strip is only available in unfinished wood that may need to be stained and finished to match the flooring.

Show us a pic.