I think I may have answered my own question through experimentation:

1. Open the file runtime.xml


2. Find the script/procedure called:

// Detecting current question mode from interaction


3. Within that script find these two lines:

if(sIntTimestamp!=null && sIntLatency==null) sMode = "continue";
if(sIntTimestamp!=null && sIntLatency!=null) sMode = "browse";


4. In the above lines change the text "continue" to "init" and also change "browse" to "init"


That seems to do it! I did not get any popups, nor did the initial learner selections display.

The only caveat seems to be that the process above should be done AFTER publishing your course, since the runtime.xml file appears to "refresh" itself when the course is in the native CourseLab format.