Selectors surprised by picking Nic Maddinson to open the batting with Travis Head in the series-opening win in Durban, the former's first test in nearly 10 years, while having opener Matt Renshaw bat at number five.
The gambit proved effective as Renshaw scored a match-winning 190 and a second-innings 82 at Kingsmead, while Maddinson chipped in a quickfire 48 in the second innings to help Australia thrash the hosts by 214 runs.
McDonald, who sits on the selection panel with George Bailey and Tony Dodemaide, said they were not set on defined roles for the batters.
"Every time that we plan out an opponent (and) surface, we're really open-minded to what our batting order can look like," he told reporters.
"I suppose the external sort of view on that is that you know you need specific orders at certain times, and this person’s an opener, this person’s a middle-order player.
“We’re more open-minded than that, but it doesn’t make it right either. So we’ll assess what we need to do going to the next test."
Former Australia captain Steve Waugh called on selectors to stop "messing around with the top order", saying it had not worked for two years.
"They've got to pick and stick now," Waugh told Australian media, adding that Renshaw should stay at number five rather than return to the top of the order.
"Don't mess around with that now. (Renshaw) has been successful, and he's comfortable, so I'd keep him there, for sure."
McDonald said all-rounder Cameron Green had yet to prove his fitness to return for the second test after missing Durban with an abdominal strain.
“Cam hasn’t started batting yet, he’s done some physical (work),” the coach said.
“So he’s got a few things to go through in the next three to four days."
Wicketkeeper-batter Josh Inglis, another potential middle-order option, was more advanced in his recovery from a broken finger.
"Josh had a couple of hits during this test match out the back of the nets during lunchtime, that’s gone well," said McDonald.