If you have multiple "Published as LTI Tool" instances and you chose the same module to publish for each, in the Deep Linking content selector it shows up multiple times so you can choose which module (and therefore instance configuration) you want to use for your remote course. This is expected and good, though it might be nice to somehow have the LTI "instance name" shown in the selector to differentiate between the duplicated modules, which seems necessary and relevant to this issue anyway.

This is not the case if you chose to publish the whole course, though. It will just show a single option of the same course, no matter how many instances have published it. It seems to use the most recently published LTI instance. 

I don't know if this is really a bug, or should be labeled as an improvement so please change it to what you think this really is.

I found the code that does this in enrol/lti/output/renderer.php in the 
render_published_resource_selection_view() function where each resource is grouped by the course ID, which is where it combines all instances that publish the whole course and inherently removes any duplicates (or really overwrites them).
 
I think it's useful to give platform instructors a choice on which instance they want to (or should) use. In my case I want instructors to be able to create different links for different groups that their students would be assigned to automatically with my custom code, but another example could simply just allowing the instructor to have a choice in whether they want grades to be synced (by having one instance published with grade syncing on, and one where it's turned off).