The very nature of restricted free agency means that good-to-great players are often going to be overpaid, which explains the Hayward and Parsons contracts (as well as earlier contracts like Eric Gordon's). I can't remember which article I read a few months back that explored this in greater detail, but it found that restricted free agents often ended up receiving extremely large raises on their next contracts relative to unrestricted free agents: something like 150% for RFAs to 125% for UFA.
Didn't read that article, but based on your memory, that analysis sounds suspect. RFAs, by rule, are players with limited experience in the NBA, who are coming off of rookie contracts and/or small contracts awarded to second-round picks. So their salaries on average will be lower, allowing for a greater percentage increase in contract. Furthermore, to be an RFA means your original team liked you enough to make you a qualifying offer, which means that the RFA pool of players won't consist of players who will have trouble finding a contract -- qualifying offers are already a substantial raise to the player's prior salary, and that's a mere starting offer. The UFA pool could certainly include players who will wind up with a salary cut in a new contract -- that's impossible for any player who's an RFA.
Maybe the analysis was more nuanced than you're remembering, but if not, it's conclusion doesn't speak to players being overpaid as RFA's, but rather them being underpaid prior to being RFA's.
The reason why some RFA's get paid more is this:
1) Team A extends a qualifying offer.
2) Team A threatens to match any qualifying offer, hoping to deter suitors and re-sign the player for less than market value. Call it the Greg Monroe and Eric Bledsoe strategy. It might have worked a little for Bledsoe -- it worked for Monroe in that Detroit gets him for cheap for a year, but he'll likely be gone next year.
3) Team B tries to call Team A's bluff and offers the player an above-market contract, because they have the money and have no better way to spend it this off-season.
4) Team A either follows through on the threat (Hayward) or doesn't (Parsons). In either case, the player gets paid a ton.
Players earning rookie extensions bypass this process, but that process still informs how each side negotiates.
Wtih AB, The Celtics started by following steps 1 and 2, but changed plans slightly in that before having their bluff called, they decided to make an offer Bradley would accept. They gave up some of the discount they might have gotten if no one called the bluff, but also got a discount on someone coming in with an offer substantially over market.
The other reason RFA's (and guys eligible for rookie extensions) get paid big is because of potential. They're young, and NBA players typically peak from about 27-30, which is at the end of most of these contracts. Especially with an extension, you're only offering a contract based on 3 years of NBA experience. Sometimes you get a bargain, like DeMar DeRozan or Rondo, sometimes you get an albatross like Tyrus Thomas, and sometimes you get a player who's paid about what he's worth.