The main problem is, that the CMD is a builder and therefore should be call independent.
Let me explain the main issue i have by implementing the logic directly in the CreateContainerCmd#withLinks method.

//will correctly create links on myNet
client.createContainerCmd(...)
  .withNetworkMode("myNet")
  .withLinks(...)

//will faulty create links on the legacy bridge
client.createContainerCmd(...)
  .withLinks(...)
  .withNetworkMode("myNet")

The issue is that the decision can't be made in the #withLinks method, because we do not know which NetworkMode is finally used.