Based on my 10 years living and traveling around SEA countries - we only stayed at non-chain hotels - I only used Agoda and Booking with about 80%/20% breakdown and never had a problem. I did have a rule to contact the hotel after booking and confirm that they had my reservation.

The only time I had a problem with a hotel was in Thailand and has nothing to do with the booking engine - it was a recently opened 4* in Phuket with not too many reviews. At the checkout, they tried to pull the traditional Thai scam - telling us that the paper tissue box in our room was ‘broken’ and wanted to charge $20 for replacement.

So make sure to read reviews carefully and look for keywords like scam, noise, problem etc… have to mention that scamming is mostly a Thai problem, you won’t see it in other countries.