When using the seamless and you include the same fields multiple times at the same level the fields will have the same field names and they are at the same level. Not only will you have trouble with conditional logic, you will also have trouble saving the data in the fields, since they both have the same name the saving of the 2nd, 3rd, etc fields will overwrite the previous values. In essence you only have one field shown multiple times. Seamless is meant for reusing the fields in a repeater or flex field where they already have some protection.
When grouped they work more like the sub fields of a repeater or flex field. The field names are prefixed, the fields have parents, and this prevents the issues.
This is all explained in the clone field documentation. See Limitations and Notes near the bottom of the page. https://www.advancedcustomfields.com/resources/clone/
