In the work done in T184251: Upgrade Select2 in Page Forms (was formerly: Upgrade JS libraries included in Page Forms): It looks like token auto-completion is not replacing but is adding to the completions available.
For example, I have a token field TF that is dependent upon a combo-box field CB, and it currently has the completion values X, Y, and Z available.
I update CB so that the completion values available would be A, B, and C.
Instead of only providing me with the options A, B, and C, it will provide me with the options X, Y, Z, A, B, and C, in that order.