Dhoni's decision to reinstate Bell came after England captain Andrew Strauss and Flower requested the Indian team to withdraw the appeal. And Flower said the English had every right to do so.
'We didn't think sitting in our changing room and fuming quietly to ourselves was going to do any good,' Flower told reporters at Trent Bridge.
'We thought communicating like that would be the way to go. We felt that Bell wasn't attempting to take a run and therefore we wanted to ask the Indian side to reconsider their appeal,' he said.
'If an England side had done that in Mumbai (against Tendulkar), I think there would have been a proper international incident on the cards. I don't think that's being overly dramatic. We've seen similar things happen before,' Flower added.
'In evaluating the situation, I don't think you should have double standards.'
England just need a couple of draws or one more victory in the four-match series to upstage India as the world number one Test side but Flower said that was not the focus for the team.
'I would like to emphasise right now that we're ahead in the series but we're only halfway through the series,' he said.
'So there is no point in triumphalism, we don't even know if we're going to win the series yet. At the forefront of our minds right now should be resting and recuperating after the back-to-back Tests and then getting our minds and bodies ready for the next challenge at Edgbaston.
'It's actually not only pointless looking further ahead than that, it's dangerous,' added.