Opening your laptop is not going to void the warranty(it's illegal to void it for that reason) and changing a thermal paste won’t void it too.
I had 2 MacBooks with Apple Care, that got their thermal paste changed, SSD upgraded and opened multiple times for cleaning service. Both of them went to Apple at some stage for some service action and never got declined for having a thermal paste changed. Of course, SSD was replaced to an original before sending for service.
Using a non-conductive and NON-TOXIC thermal paste like MX-4 won't cause any shorts if too much was applied. I see 2005 forum threads about thermal paste being toxic, but nothing that proves it for new thermal compounds currently available(except liquid metal).
In my opinion, Apple is applying too little and poor quality thermal paste on CPUs. Changing it will only help your machine be more thermally efficient in a long run.