Leto II used all the major factions to his purposes during his reign, and in forcing them to work 'for him' in certain ways he therefore also made it so that they were inadvertently working with each other for common purpose for the first time. From their perspective it probably seemed more like him subjugating them, but the Tleilaxu always seemed to me to be beyond the other factions in recognizing certain intricacies. Take, for example, Scytale's famous conversation with Mohiam and Edric in DM where he describes the BT experiment with their KH. Unlike the BG, the BT not only knew what a KH was really about but also examined what it would be like to be one and how to stop one. The BG, prior to Paul, seemed comparatively clueless from what we can see.
Similarly, I think the BT would have been able to see through Leto II's 'subjugation' and somewhat understand what he was trying to do, compared to the other factions that merely endured his reign. They, too, were long-term planners, and probably respected him for that. That they eventually determined how to produce spice may or may not have even been a project secretly commissioned by Leto II in the first place, since he knew they'd be the only ones equipped for such a task. I don't think Leto II kept them around 'just because they had their uses,' though.
Consider the Duncans, who, it turns out, were a crucial part of the events that later unfolded in the series. The Duncans eventually made way for the CH:D Duncan who could do what he did. Did the BT foresee this eventuality, or at least hope for it, much in the way they hoped for the final result they got with Hayt? My guess would be yes, and my guess would also be that Leto II did as well. I see the breeding and progression of the Duncans as being a combined effort between the BT and Leto II to produce a certain result, part of which was to propagate the Siona gene when the time was right, but another part being the eventual creation of a Duncan-whatever-he-is in CH:D. I sincerely doubt Leto II kept Duncan around just to amuse himself or for Atreides nostalgia, because then he could just as soon have picked Gurney or others to bring back as gholas. This brings up the question of what, exactly, the final Duncan was. Was he a tool that would teach them how to defeat the New Face Dancers that would eventually lead to Marty and Daniel (this would mirror the use of their KH, who was a tool to teach them how to defeat Paul)? We don't know how early the masters came up with or knew of the possibility of NFD and that Marty and Daniel could come to be. M&D claim that the masters could never have thought that a NFD could become independent, but I give the masters more credit than that.
If, as I suspect, Leto II and the BT were guarding against an eventual problem with the NFD, and if, also, we can agree that Leto II deliberately helped them to achieve a new level of ghola-tech, much as Paul unwillingly did by way of Hayt, then we could see why the BT would revere him as a prophet. It would mean that Leto II was perhaps the only powindah ever to be privy to some of their secret planning and to even partake in it and help out. None of this is 'fact', as such, but so many of the events in this series happen behind the scenes that some connecting of dots is needed, even at the risk of having to engage in conjecture sometimes.