ISTM that the advantages of plastic tubes are apparent. They don’t keep their shape, and so don’t get all gnarled up and impossible to empty, and they are also less likely to spring holes from repeated bending. But a lot of ointment is sold in metal tubes, so there must be some advantage there too. What is it?
Only thing I can think of is that perhaps some things store better in metal.
It’s mostly for health regulations. Some things need to be sterilized, which involves heating them to temperatures much higher than what a plastic tube can tolerate.
Some materials do interact with the plastics that they typically use as well.
Also, metal is an absolute barrier to moisture.
I disagree with you about being able to squeeze more out of a plastic tube. A metal tube that you are able to flatten will yield a higher percentage of the contents for use, which is important with prescription ointments.
Well that probably depends a lot on how you squeeze it. If you’re careful to squeeze from the bottom up, in a symmetric fashion, that’s probably true. If you - or your spouse 
- are the type to just randomly squeeze from the middle or top, then it’s very much not so.
Or, you can do what I do - squeeze the middle, then when the thing is getting hard to squeeze, set it on the counter and roll the tube flat from the bottom with a shaving cream can so that you have all the contents up at the front of the tube. Repeat as needed until there isn’t anything extractable left in the tube.
WAG: Plastic tries to spring back to shape, and as it does so, it sucks air. This may be undesirable for certain types of substances. Metal tubes don’t try to suck air into it.
I would also assume that some ointments need better protection from oxygen permeating into the tube than most plastics can provide.
Besides, you are looking at it the wrong way.
Not being able to get all of the contents out of the tube is a good thing because then they will have to go back an buy more sooner!