You're quite right. If you actually read the Shang et al 2006 paper you'll discover that homeopathy was discovered to be better than placebo but less good than the best conventional treatment. The PR and media coverage around the paper missed this entirely. The Ernst paper mentioned by the article also could not determine if homeopathy was entirely due to placebo. Its worth noting that this is the current state of scientific knowledge regarding homeopathy. It appears to be somewhat better than placebo judging from meta analysis.
Now, this doesn't mean its real (or fake), it just means we need more research. Its also worth noting that the trials of homeopathy in the Shang 2006 article were rated as higher quality than those of conventional treatment (but there were less of them).
When there was more than one conventional treatment trial matching a homeopathic trial, they randomly selected the conventional treatment trial. They did not inject any notion of 'best' conventional treatment.