Hi there. SuperTiled2Unity puts the pivot point for Tile Objects at the bottom-left corner because that's what Tiled does.
If you need to manage the pivot point of a Tile Object then chances you want to control or manage other aspects of the object. In other words, it's now longer just a decorative tile on your level somewhere but tied into gameplay somehow.
In that case I'd recommend keeping your Tile Object in Tiled but use a "Prefab Replacement" so that those objects are replaced by a "proper" sprite (or some other object) that you have scripting control over.
You can read about Prefab Replacements in SuperTiled2Unity here:
https://github.com/Seanba/SuperPrefabReplacement