@ahenry75F7H
For instance, if an architect puts multiple buildings into one linked revit model and the link is put into the central model. All I see under the visibility settings is the linked model rather than all of the individual buildings.
As I understand your problem is related to the architect's decision to "Attach" their linked individual building project files (which I will call Project B1, B2, B3) in a main site file (which I will call Project A) that you are linking into your mechanical project file (Project M). Effectively, your ability to change visibility graphics of files B1, B2, etc in your project file will be very limited.
In a consultant team meeting, you could suggest that all project files be "Overlayed" and a shared coordinate system set up. With the project already underway, this will require more work that if it was done from the start. In this solution, your project M will have each project M, B1, B2, etc as seperate links project files allowing you to control them through the main visibility graphics settings or individually for each linked file through the linked project graphic settings.
If changing the link type and rebuilding the links with share coordinates is unavailable, you could ask the architect to include view layouts with graphic overrides that will live in project M, setting display as required by the mechanical views and then assigning the link graphic override to use the appropriately named linked view.
The purpose of this is to be able to work on the piping of individual buildings without having the views be obstructed by the surroundings.
This statement makes me think that you are having problems that project B1 is hiding project B2 or vice versa in a specific view. This could be solved by asking the architect to have individual dedicated worksets for each linked project in their main project M file (If they don't already do that). In the offending view, you can then set the linked project graphic override to hide the workset of the building project file.
Hope this helps,
-luc