As a native speaker, I wouldn't use transparent in this context. While the two words are related, there's an extra implication brought in by transparent, and that's of "otherwise hidden".
This implication comes from the other meaning of transparent. For example, a pane of glass is transparent. That doesn't mean that the pane of glass is obvious (actually, the more transparent a pane of glass is, the less noticeable it is) but it does mean that whatever lies behind the pane of glass is visible through the glass and is not hidden. Something being transparent means that something that lies behind it is no longer hidden by it and is now apparent.
This implication carries through to the metaphorical usage. "The residents will see through any transparent attempt to buy their votes" - there's the implicit assumption that buying votes would normally be hidden, as it's a bad thing. The fact that the attempt is transparent means that assumed hiding is absent or ineffective, and the motives behind the attempt are apparent and no longer hidden. Likewise with "transparent nonsense" the implicit assumption is that people are trying to hide nonsense, and having the nonsense be transparent means you can see through that weak attempt at hiding it. It's less about being obvious from the outset than about being revealed.
In your case, "the quality online may not be so transparent" doesn't really carry any direct implications of hiding. "Quality" by itself is neutral, and there's no implication from it or the rest of the sentence of it being bad or good. The quality not being apparent here means you're taking a risk, not that someone is attempting to hide something.
However, a little different formulation pulls in the implication of hiding and transparent becomes okay: Online sellers are not transparent in reporting the quality of their goods. or These items are of transparently poor quality. For the latter, the implicit assumption that sellers will attempt to hide the fact that goods are poor quality pulls in enough sense of "revealing" that transparent becomes acceptable.
As to apparent and transparent being listed as synonyms in the dictionary, it's very important to realize that "synonyms" do not mean "identical". It's a fallacy that a lot of native English speakers also make, but it's just not true. Two words being synonyms just mean they share similar or related meanings, not necessarily identical ones. Different words have different implications and different usages, meaning you can't just blindly swap them. (Though in many cases either of a pair of synonyms do work.) Dictionaries provide lists of synonyms as an aid to help people find one of a related set of words which best captures their meaning. It's not a license to randomly swap them.