Grigori
My understanding was the Golden Dawn switched Strength and Justice for astrological reasons, and this switch was maintained by Waite in the RWS deck and presented as his own idea (the GD deck still being a secret one, and from recent readings it seems Waite had a hand in the designing of the GD deck and its concordances anyway, despite the story that Mathers produced it "magically" already complete in the first instance).
Crowley returned them to their previous order (as in the TdM) which put the signs Leo and Libra out of order again. This justified his exchanging Tzaddi and Heh, between the Star and the Emperor (by having a pair out of synch in both the astrological and the cabala concordances)
So while the Thoth deck does use the order of the TdM, it is also a considered deviation from the GD tradition, and not just a return the TdM tradition (as is evident from the other changes he made e.g. the Courts which are decidedly GD in nature, much more so than the RWS which is closer to the TdM)
Crowley returned them to their previous order (as in the TdM) which put the signs Leo and Libra out of order again. This justified his exchanging Tzaddi and Heh, between the Star and the Emperor (by having a pair out of synch in both the astrological and the cabala concordances)
So while the Thoth deck does use the order of the TdM, it is also a considered deviation from the GD tradition, and not just a return the TdM tradition (as is evident from the other changes he made e.g. the Courts which are decidedly GD in nature, much more so than the RWS which is closer to the TdM)