One note, with Betaine HCl, you get the Betaine part, and that has many health benefits.
I don't remember the exact reasons, but it is related to the neurotransmitter Choline. It is said to be good for the liver, and it is good for the immune system. It is a methyl donor, and this methyl group participates in many reactions in the body. It elevates level of SAMe, an antioxidant.
There is a lot of info about histapenia, histadelia and methyl donors but it gets complicated.
Also, some websites claim that MSM "neutralizes" stomach acid, which in my opinion means that it raises (or regularize) stomach acid and thus remove the causes of acid reflux. I'm not sure if MSM is really as good as what is said on the Net... Too good to be true.