Try configuring your application so that it runs with UIAccess=true and with a window that is WS_EX_TOPMOST.
In order to run with UIAccess it must be properly manifested, signed and loaded from a secure location (e.g., C:\Program Files..., C:\Windows\System32).
In my quick and dirty test a Windows desktop application was able to place itself in the Z-order above other windows. It always appeared above windows (even TOPMOST) of other applications that did not have UIAccess privileges. But there is no guarantee that it would always appear over TOPMOST windows created by other UIAccess enabled applications.