I would like to know if Houdini 15 will provide any updates for Houdini Indie Engine to resolve issues with dlls where the same dll is used by Houdini Engine but a different version of that dll is used by the Application trying to integrate Houdini Engine.

Yep. We're actually adding a way to have Houdini Engine run in a separate process. This would avoid any library clashes between Houdini and the host application.

In your host, you'd just link against a small library we will ship that will be able to spawn and communicate with the Houdini Engine (server) process via pipes or over the network.