Best practice is architectural Client needs to lead/establish with all disciplines to be on the same location. We use all methods and still do a plan view coloring visual review of all columns.
Structural Columns should lead, Arch client will need to be the one copy/monitoring our structural columns, anything structural (Loads)
Once you link in architectural model, you should be aligned for the remaining of the project.
Sometimes other disciplines may not be aligned and that is sometimes the issue , but should been resolved by architectural PM coordination for all disciplines to do so. If when that occurs we manually correct the link, once is set, any future versions of third party model can be reloaded from, even if they have a new different file name. This will keep it in the same location.