Which are the most underrated universities in Europe to earn a PhD in Life Sciences? Getting into a program within countries like Germany, France, Netherlands is tough. Which other countries have a higher acceptance rate?

This is nonsense for me. If you really believe in rating, do not go for low rate one. In South and East Europe funding opportunities are limited especially for non-EU students.

I guess the OP means underrated as in a good uni that isn't necessarily ranked highly. I wouldn't know the answer to the question though. I guess it might be worth thinking about what is stopping you from getting accepted where you want to be accepted. Have you tried?

If you want to game the system, you need to do a lot more research. I agree that there are a lot of underrated universities that might be easier to get into. However the underrated universities will have specialities in different fields, subfields, or specific topics. My university has world class lung function group in an otherwise mediocre life science department. That trend will be replicated throughout Europe; mediocre university but contains a couple of world class research groups.

So if you want to game the system; choose a topic, research it extensively, look at the university affiliations on highly cited papers and then apply there. I don't agree with this strategy but it might work.