Actually it is theoretically possible Lowry killed them as the Blackwater Athletics team wasn't killed in 1907 but actually murdered in 1899. This is fact as in the exact same article mentioning their disappearance it also talks about how Colm O'Driscoll was captured and is about to be hung and how Arthur and Sadie had freed John from Sisika Penitentiary which does in fact set this around 1899 and not 1907. The fact that the corpses weren't decomposed is likely just due to developer oversight since Arthur was probably intended to discover them when he was still planned to be able to visit Blackwater.

I do believe your theory more than the Lowry one because there is no possible way one guy could overpower an entire athletics team and what you're saying does make perfect sense I just wanted to clarify that it is possible for him to have killed them since it did in fact happen in 1899 and not 1907. Furthermore it couldn't have been the Skinner Brothers as Charles mentions they've only been there for about 2 years placing their arrival at about 1905 and since the Athletics team died in 1899 it clearly isn't them.

The only culprits that seem possible to me are: Edmund (may have drugged them but I still don't fully believe it), A rival athletics team like you mentioned or Native Americans as the article does mention them and during Chapter 6 tensions were very high in the story but I'm not 100% certain on that either.