Whatever the authorities believe in the early days they will be keen to recover the disappeared child as this will yield the greatest clues as to what exactly happened.
I've holidayed on the Algarve a couple of times but never really ventured inland. Going by Google satellite it appears one could take an inland route from PDL to Faro (airport) and hit some sparsely populated areas?
I'm not sure where you are heading with this thought, so I'll try splitting things down.
1. There are two routes from Luz to Faro. The older route is the EN125, which runs through a lot of towns and villages. The newer route is the A22, a motorway which goes through nothing. The T9 would all have used the motorway on journeys between Luz and Faro.
2. Portugal is part of the Schengen Zone, which covers most of Europe. It means you can cross borders without being checked. So one can drive along the A22 and enter Spain without hinder. That might take perhaps an hour and a half from Luz, to enter a foreign country with a different police force.
3. If you are thinking of body concealment or disposal, anyone with knowledge of the terrain around Luz would know how to achieve that with ease. I now live inland from Luz, on a plot large enough to make MBM disappear, even if a thorough police search was conducted. There are hundreds or thousands of such plots.
Hopefully I have covered all bases.