I don't know that many people would be confused. Someone who is digging far enough into indie RPGs on Steam to play both yours and the other one is probably already aware of purchasable assets, although they may or may not approve of using them. If someone does accuse you of improper use, it is easily refuted. I agree with technicat that the best practice is to credit anything you didn't make yourself, even if you are not technically required to do so.
As for what people will think of it, opinions vary. In part it depends on how you use them. Hardly anyone will notice a reused brick or grass texture (I'm sure AAA studios do this all the time), but something like a character portrait benefits a lot more from being unique to your game. Other stuff like GUI elements and monster models are probably somewhere in the middle. As you already noted, some very popular games like Tales of Maj'Eyal and Realm of the Mad God use non-proprietary assets. RPG Maker games on the other hand are frequently criticized for "all looking the same" as many of them pull from the same set of stock assets.
Unfortunately it is probably the case that a lot of people will mentally associate recognizable assets with the most recognizable game that uses them, although like I said, how much people really care about that will vary. Ultimately this is just the tradeoff for using stock assets: you save time, but lose distinctiveness.