[Lombra]

I use the following to modify the time format and have not had any problems as far as I remember.

local function lSetTimeText(button, timeLeft)
	local d, h, m, s = ChatFrame_TimeBreakDown(timeLeft)
	if timeLeft <= 0 then
		button:SetText("")
	elseif timeLeft < 3600 then
		button:SetFormattedText("%02d:%02d", m, s)
	end
end

hooksecurefunc("AuraButton_UpdateDuration", function(auraButton, timeLeft)
	if SHOW_BUFF_DURATIONS == "1" and timeLeft then
		local duration = auraButton.duration
		lSetTimeText(duration, timeLeft)
	end
end)

But I realise that that wasn't necessarily your point.