When we use beam end offsets it ignores the section Offset. Does this affect the model or it is merely visual?

If the beam end offset function is used along with the section offset, then the section offset will be automatically changed to Center-Center. This affects the model as well as visualization. Also, tendons cannot be assigned to the elements to which Beam End Offset is assigned. 

As a workaround, removing the beam end offset and creating an elastic link whose type is 'Rigid' for the corresponding offset length is recommended, as shown below. The element needs to be divided at the end of the offset region, and then you can create the elastic link.

Regretfully, there is no option to show the element's non-offset portion. It always shows the entire element. This is an interesting feature to be considered for future development.