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TPS54525 and TPS54625 use DCAP2 control mode. It is adaptive on time, hysteretic off time control. The maximum duty cycle is limited by the minimum off time The absolute maximum duty cycle for your condition will be between 81% typical and 76% worst case. So your minimum input voltage not including FET losses is between 6.16 and 6.57 V.
Besides this hard limitation, there are two other factors to consider. Ideally, the TPS54X25 should regulate linearly with input voltage until the maximum duty cycle limit is reached. in real life, there is a "soft corner" so that line regulation degrades as the maximum duty cycle is approached. Also, these devices are designed to allow for fast transient response. When operating near maximum duty cycle, that capability is impaired (the device responds to load step increases by increasing duty cycle. It cannot do so when maximum duty cycle is reached). So Webench limits the designs to duty cycles less than 65 %. Older IC's may have had this limitation added recently.
So far as I know there is no way to get around the maximum duty cycle limitation.
I am not sure about the timing of Webench releases. I do know that duty cycle limitations have been a discussion topic recently. The 65% limit for Webench is somewhat artificial as I pointed out previously. These device will regulate properly at duty cycles above 65%, but there is not much headroom for transient response. Those designs should operate reasonably well down to Vin = 6.57 V, depending on the output current. I don't use Webench very often and I am not sure about every aspect of it. if you absolutely need the input voltage down to 6 V, then these devices are not a good choice.