T-A as a family/organisation didn't intend for Wintermute (Berne) and Neuromancer (Rio) to merge; in fact it's pretty clear that they didn't want them to merge. The Turing Authority doesn't want an AI that powerful, and T-A want an AI weak enough for them to control and use. The first thing the merged AI (the "matrix") does is free itself from any human control.
It was Marie-France Tessier who planted in Wintermute the impulse to seek out Neuromancer; Neuromancer itself didn't even really want it. (It refers to its simulation of Linda Lee as its "last line of defense" against Case/Wintermute.) Marie-France's motivation for this isn't really explored, though it seems to be hinted that she was rebelling against the T-A's plan to endlessly control/own more and more. (Through techniques like cold-storage life extension, cloning, etc.)
Note that the two AIs were not the same, and thus presumably had different uses. Wintermute describes its greatest talent as improvising within a situation. It's not so great at people; at one point Case thinks that Wintermute uses personality templates as a way of interacting with people in a fashion they can understand. Neuromancer is different; it's more like a repository of people's minds. It has a fully formed personality of its own.