An important point about racing cars is how completely their performance is determined by the rules of the series. Hybrids dominating says more about the details of the rules than about hybrids.
By design, the LMP1 rules permit a diverse range of solutions. Porsche run a turbocharged V4 petrol engine, Audi use a turbocharged V6 diesel, Toyota a naturally aspirated petrol V8. Audi's hybrid system has half the energy capacity of Porsche's. Teams running a large hybrid system are penalised with a lower fuel rate limit and vice-versa.
The technical regulations are significant in any racing formula, but the LMP1 rules are carefully balanced to prevent the dominance of any one technological approach. Diesel engines have been significantly gimped in recent years to curtail the dominance of Audi.
None of what you said is wrong, but it also doesn't refute the central point: current WEC regulations are very much designed to make the LMP1 hybrid formula the premiere class. While there is a non-hybrid LMP1 formula, it is a distinctly lower performance class which exists to accommodate privateer teams who can't afford a complex hybrid system.
Since Le Mans is an endurance race, the vehicles that can run longer with less pit stops have a strong advantage. This is what the Audi diesels dominated for a good part of the 2000s.