Molineux's extensive injury history meant eyebrows were raised when Cricket Australia unveiled her as the retiring Alyssa Healy's replacement ahead of vice-captain Tahlia McGrath and star allrounder Ash Gardner.
Bowling allrounder Molineux has played for Australia since 2018 but injuries sidelined her for more than two years from 2021, before she missed the most recent Ashes with a knee issue.
Injury problems resurfaced during the recent multi-format series against India as Molineux took on the T20I captaincy.
A back issue meant she neither bowled her spin nor batted as captain in the first two matches of the subsequent multi-format tour of the Wests Indies, and eventually missed the last two to rest.
Flegler said the latest setback was "not ideal" but that the plan had always been to take a conservative approach to Molineux's fitness ahead of this year's T20 World Cup.
He nevertheless acknowledged it was "unprecedented" for Australia to bestow the captaincy upon a player subject to such uncertainty around her fitness.
"It's probably a fair point to say it's unprecedented, but we think on balance, she was the candidate that was the best option for a number of reasons," he said.
"Her on-field experience and success that she'd had, and her off-field connection and a vision for the team."
Molineux will take part in upcoming training camps with the squad and is on track to be fit for the World Cup that begins in the UK in June.
Flegler has not had any second thoughts about the captaincy decision, though he conceded Australia would have to remain open to change should more long-term injuries arise.
"We're comfortable internally that it was the right decision for this group at this time," he said.
"We're happy to be judged on that down the track. If it turns out that Soph is injured again long-term, we'll have to reassess where we go with the captaincy.
"But it wasn't just one meeting, let's make a call on something, there are lots of discussions that take place, and not just among selectors ... (but) I totally get that it might seem a bit odd from the outside."
Flegler's comments come as Australia revealed its national contract list, which features uncapped Chloe Ainsworth and teenage allrounder Lucy Hamilton for the first time.
Hamilton, 19, has made her Australian debut in all three formats since the beginning of March, while fellow allrounder Ainsworth is viewed as a longer-term prospect for the international side.
Tayla Vlaeminck and uncapped Tess Flintoff did not have their contracts renewed, though Vlaeminck returned to the field in the 'Green vs Gold' domestic match this week after more than 500 days out with a shoulder problem.
